49ers defense makes its stand in 26-21 win over Eagles (w/video)

SANTA CLARA - When is a defensive shutout not enough? When your special teams and offense give up three touchdowns, and your opponent has finally figured out how to move the ball, and it’s first-and-goal from your 6 with 2:50 left in the game and you’re clinging to a 26-21 lead.

That was the predicament the 49ers defense found itself in Sunday at Levi’s Stadium, through almost no fault of its own. But with the team staring down the barrel of a 1-3 start to the season, the D rose to the occasion and kept the visiting Philadelphia Eagles out of the end zone, preserving a desperately needed 26-21 victory.

“The defense turned in a real gem,” 49ers head coach Jim Harbaugh said. “They were getting off the field early in the possessions.”

That’s especially important against a team like the Eagles that relies on tempo, wearing down defenders with a no-huddle offense that makes substitution difficult.

San Francisco defensive coordinator Vic Fangio inoculated his players to that fast-paced attack at Friday’s practice. NFL Fridays are usually devoted to situational plays like short yardage and red zone. This time, Fangio intentionally stressed his guys with accelerated snaps and lots of noise.

“It was crazy,” cornerback Perrish Cox said. “Coach, a couple plays, he’d send us on a deep post, and the very next play they’d already have a play with another set of receivers lined up. You’d have to run back, get the call lined up and go ahead.”

“It was very loud,” strong safety Antoine Bethea added. “(Fangio) was calling in calls real late so the players would have to kind of scramble to get in their places and communicate. So made it real easy for us … on Sunday.”

The Eagles would finish with just 213 total yards and a mere 22 rushing yards. LeSean McCoy, Philadelphia’s elusive running back, wound up with 17 yards on 10 carries, and didn’t have a reception.

By midway through the fourth quarter, the Eagles hadn’t crossed midfield. But starting from their 9 after a penalty on a kickoff, and trailing 26-21, their passing game finally started to click. Following a brilliant, reaching, diving catch by Jeremy Maclin at the sideline, then an 11-yard reception by Jordan Matthews, Philadelphia was looking at first-and-goal from the 6.

On first down, Eagles quarterback Nick Foles saw no one open and threw the ball away. On second, Bethea made a huge tackle on a stretch draw by McCoy and tackled him just inside the 49ers’ 2. With the Niners already trailing Arizona and Seattle in the NFC West, the next play or two could help set their course in 2014.

Again, Fangio’s preparation was the difference. The 49ers had focused almost exclusively on two Philadelphia plays in practicing goal-line defense this week. Those were the two plays Philadelphia coach Chip Kelly dialed up.

On third down, Bethea blitzed from the right side of the offensive formation and forced Foles into a hurried incompletion. On fourth, the quarterback rolled right and threw to Maclin at the back of the end zone, but the play was well covered and the pass sailed high.

The Eagles had one more chance, getting the ball back with 1:23 to play. But they were out of timeouts and backed up to their 31 after a penalty for an illegal block on a punt. They lost 14 yards on a holding call and a poorly designed swing pass, and Foles’ final pass was intercepted by Cox to ice the game.

The 49ers spent most of the game digging out of a hole, because the offense and special teams kept finding ways to give up points.

The trouble started 2:37 into the game when San Francisco had to punt from its 2-yard line and Philadelphia’s Trey Burton shot past Dan Skuta on an inside rush and blocked Andy Lee’s kick. The Eagles’ Brad Smith fell on the ball in the end zone for a jolting touchdown.

The 49ers fought back to take a 10-7 lead early in the second quarter - then gave it back. Operating near midfield, quarterback Colin Kaepernick locked in on wide receiver Brandon Lloyd on a slant route and never saw safety Malcolm Jenkins, who picked off the pass, slipped a couple tackles and went 53 yards for a touchdown.

The Niners got the ball again, punted again, and Darren Sproles, Philadelphia’s 5-foot-6 dynamo, returned it 82 yards down the right sideline for a touchdown to give his team a 21-10 lead.

“The one, put the ball at the 1-yard line, made the team punt, that was not ideal,” Harbaugh said.

“Somehow we got two rushers on Skuta. I don’t know exactly how that transpired. We’ll shore that up. And I don’t know how we got out-leveraged and gave the return on the boundary as well. We’ll get it corrected.”

The 49ers added a field goal by Phil Dawson late in the second quarter - he was perfect on four attempts that ranged from 29 to 51 yards - and finished the half with Justin Smith’s fumble recovery. They went into the locker room trailing 21-13.

“At halftime it was still an eight-point game,” linebacker Ahmad Brooks said. “As much as they did, as much as we did, it was out for grabs for us to go ahead and get the win.”

The defense came up with three more takeaways in the second half: a ball that was stripped from tight end Zach Ertz by Bethea and popped right into Cox’s arms, an interception by Bethea and Cox’s final theft.

Meanwhile, the Niners made it a one-point game on Stevie Johnson’s picture-perfect tiptoe catch in the end zone, took the lead on a Dawson field goal late in the third quarter and added another with 6:38 to play.

The 49ers had looked surprisingly erratic over the first three weeks of the season. Honestly, they looked pretty erratic Sunday, too. But they showed that, on occasion, they still can muster the resilience and hard-hitting defense of a playoff contender.

You can reach staff writer ?Phil Barber at phil.barber@pressdemocrat.com.