Fletcher Cox comes up with one of the Eagles four sacks against 49ers QB C.J. Beathard . Photo by Andy Lewis / contrastphotography.com

The Eagles game against the winless San Francisco 49ers went pretty much the way most people thought it would.

The home team was at least three touchdowns better than the 49ers and when it was all over, the 33-10 score at the rain-soaked Linc showed the predictions were accurate.

But it wasn’t pretty and it wasn’t easy. The game also raised questions about the offensive line going forward.

The Eagles (7-1) offense took San Francisco’s best shot throughout the first quarter and until just before the two-minute warning of the first half when the score was just 3-0 Eagles.

The Birds couldn’t run the ball and had trouble with pass protection. Carson Wentz was sacked three times and rushed for just 28 yards on 13 carries.

Part of it was using a new left tackle, Halapoulivaati Vaitai, who started in place of All Pro tackle Jason Peters, who is out for the season with a torn MCL and ACL. Vaitai is in his second season out of TCU.

Part of it was what the 49ers were throwing at the Birds: constant blitzes and looks they had not seen from San Francisco on film earlier this year.

“We’re seeing blitz quite a bit,” head coach Doug Pederson said at his press conference after the game. “I think we’re probably the number one team, offensively, that’s being blitzed in the NFL right now. Teams are just coming after us, I think, to probably put pressure on Carson. We’ll continue to see it, and we’ll continue to work at it. I don’t know if it necessarily disrupted Carson. Obviously, it made him move around a little bit in the game. But later on, we were able to fix the protection. He used his backs a little bit more out of the backfield, and then even sometimes the run game, trying to keep us in some third and shorter distances, we were able to convert. But I think we were 4 of 14 today, and really that’s not good enough for us. We’ve got to get better.”

To Pederson’s point, the Eagles did keep Wentz upright in the second half, but he was under pressure the entire game.

The Eagles defense kept the 49ers in check most of the afternoon, holding the visitors to 94 yards rushing on 24 carries and no rushing touchdowns.

Rookie quarterback C,J, Beathard was 17 of 36 for just 167 yards and a touchdown pass. Beathard was intercepted twice including a pick-six and finished with a quarterback rating of 46.9.

The Eagles scored their first touchdown of the game with 1:51 left in the second quarter.

Wentz took the Birds on a six-play, 56-yard drive that included a 24-yard pass the rookie wide receiver Mack Hollins and a 24-yard pass interference call on 49ers cornerback Dontae Johnson who was covering Torrey Smith.

Wentz hit tight end Zach Ertz in the middle of the end zone and the score was 9-0 as Elliott missed the extra point.

On the third play of the ensuing drive that started at the 49ers 25, Beathard’s short pass to the right intended for Pierre Garcon, was picked off by cornerback Jalen Mills who caught the ball at the 37-yard line, then zig-zagged his way to the end zone. Pederson went for two and Wentz hit Alshon Jeffery in the back of the end zone. The score was 17-0 with 1:24 left in the half.

At his locker after the game, Mills smiled and admitted the big guys wearing 49ers uniforms gave him the mindset to make it to the end zone.

“Actually I was thinking about going out of bounds till I seen all those O-lineman,” Mills laughed. “And you don’t want to get hit by those guys, it hurts for sure. Then something just clicked in my head..hey go score.”

Mills then was serious about what was going on in the game. The entire game had been played in the rain, San Francisco’s blitz was having an impact on the Eagles ability to move the ball. The Birds did have an interception by Rodney McCleod earlier in the quarter but the 49ers were hanging around.

“At the same time, we needed a spark,” Mills said. “The rain, we kind of started slow as a defense, we kind of started slow as an offense. This (game plan) wasn’t kind of kicking, we wanted to get the fans into it. We needed a spark and I was just trying to make a play for the team.”

Mills said he also did not want to face his teammates and coaches if he did not make his interception into a highlight of the game.

“I’ve been getting grilled all week from (defensive coordinator Jim) Schwartz, coach Cory (Undlin), Malcolm (Jenkins) and Rodney (McLeod) about having no return skills on my first two interceptions,” Mills said. “So that was definitely my mindset.”

The 49ers moved the ball pretty well but ran out of clock. On a Hail Mary toss by Beathard on last play of the first half, 6-foot-3 Jeffery, who was inserted into the game for his length, broke up a potential TD pass to Kendrick Bourne.

Neither team moved the ball to start the third quarter.

The 49ers particularly had a hard doing anything when they lost Pro Bowl left tackle Joe Staley for the game and possibly the season when suffered an eye injury at the end if the second quarter .

San Francisco had backup Zane Beadles at left tackle and he was not effective at all. Staley, 33, was the center of trade rumors with the Eagles to take the place of injured Jason Peters.

On the Eagles third drive of the third quarter, they were able to move the ball to the 49ers 32-yard line where Elliott to hit a 50-yard field goal and make the score 20-0.

Wentz’ only big mistake of the day came late in the third quarter when, on a third and 14 from his own 22-yard line, 49ers corner Ahkello Witherspoon was able to get in front of a Wentz pass intended for Mack Hollins.

On the first play after the interception, Beathard hit Matt Breida with a 21 yard touchdown pass and suddenly it was 20-7.

The rookie out of Colorado talked about the play.

“It was man coverage on third and long,” Witherspoon said. “Going into the week, some of their third-down concepts, dig routes. I was just planning on one anticipating the dig route and he ran it. I just timed the ball right.”

The Eagles struck back with a three-play drive on their next possession. After an incomplete pass, Corey Clement ran for 22 yards. Then Wentz hit Jeffery with a pass he ripped away from cornerback Rashard Robinson at about 30-yard line, and powered his way into the end zone for 53-yard completion making the score 27-7.

The Eagles’s final touchdown came on a Blount 12-yard run with 10:22 left in the fourth quarter. Elliott missed another extra point on the soggy field, but he did hit field goals of 40 and 51 yards.

By the fourth quarter 49ers defense was finally gassed.

Center Jason Kelce said the only way teams seem to be able to slow the Birds offense is to gamble with pressure.

“I think when teams haven’t blitzed us we’ve had tremendous success,” Kelce said. “We’ve been one of the most dynamic offenses in the NFL up to date. And really if you looked at it, I think we’ve done a good job of beating the blitz as well. If there has been anything, there have been certain games where teams have blitzed and slowed us down, we just need to do a better job. It’s not just blitz pickup, it’s getting into good run calls, it’s getting into the proper angles and techniques for what you’re getting on defense. But it’s also kind of optimistic that we’re getting this now so now we can continue to learn and continue to grow. Teams are going to continue to pressure us cause, really the only thing that’s slowed down our offense to date is when teams have given us funky looks or pressures to stop out run game. We’re going to have to be able to have answers for this moving forward and I’m optimistic about that really.”

Mills said they will have fun with the win Sunday night, but that’s it.

“The game just ended, of course we’re going to enjoy it the right way, safely,” Mills said. “But once we step back into that building on Tuesday, we’ll watch the film and get the corrections, then our mindsets are on the Broncos and nothing else. One game at a time, one week at a time and our emphasis this whole year is being 1-0 after each and every week, don’t look forward to anybody.”