SANTA CLARA –- The up-tempo, explosive Philadelphia Eagles offense was the least of the 49ers’ concerns on Sunday.
The 49ers surrendered two touchdowns on special teams and one more on a Colin Kaepernick interception in the first half. But Vic Fangio’s defense camouflaged the 49ers’ other shortcomings with an incredible showing.
And the 49ers’ offense made just enough plays to end a two-game skid with a 26-21 victory over the previously unbeaten Eagles on Sunday at Levi’s Stadium.
The 49ers’ defense was outstanding throughout Sunday’s game, as Chip Kelly’s fast-pace offense was slowed to crawl. They did not move into 49ers’ territory for the first 55 minutes of the game.
The defense’s final stand came inside the two-minute warning when the 49ers’ held on a fourth-and-goal situation from their own 1-yard line. Rookie Aaron Lynch chased Eagles quarterback Nick Foles out of the pocket to force an incomplete pass out of the back of the end zone.
[MAIOCCO: Vernon, Anthony Davis out with injuries]
On the next series, Lynch dropped Darren Sproles for a 4-yard loss on a screen pass. Perrish Cox cemented the victory with an interception on a fourth-and-20 play with 40 seconds remaining.
That kind of defense was exactly what the 49ers (2-2) needed, coming off confidence-testing losses to the Chicago Bears and Arizona Cardinals in back-to-back weeks.
The 49ers returned to their proven formula of playing strong defense and featuring the run game. Frank Gore, the franchise’s all-time leading rusher, led the way with 119 yards on 24 rushing attempts.
And quarterback Colin Kaepernick added 59 yards on six attempts. He completed 17 of 30 passes for 218 yards with two touchdowns and one interception.
Meanwhile, the 49ers put the clamps on LeSean McCoy, a 1,600-yard rusher last season, who managed just 17 yards on 10 carries in Sunday’s game. Foles completed just 21 of 43 passes for 195 yards and two interceptions.
The only offense Philadelphia was able to generate came in the offense -– and in unique ways.The Eagles, who have been slow-starters this season, got quite a jolt from their special teams and defense in the first half.
With the 49ers lined up to punt from their own 2-yard line, the Eagles went for the block. Trey Burton got penetration as the 49ers’ Dan Skuta found himself attempting to block two players on the play. Burton blocked Lee’s punt, and Brad Smith recovered it in the end zone for a touchdown.
After the 49ers took a 10-7 lead, the Eagles’ defense was next in line to score.
Kaepernick tried to hit Brandon Lloyd on an in-cut, but he failed to notice safety Malcolm Jenkins in the path. Jenkins recorded his third interception in three games and meandered his way 53 yards for a touchdown.
The Levi’s Stadium crowd grew even more restless a short time later when Darren Sproles eluded 49ers gunner Kassim Osgood and returned a punt 82 yards for a touchdown to give Philadelphia a 21-10 lead with 8:49 remaining in the second quarter.
The 49ers rallied back and eventually took a 23-21 lead with 3:33 remaining in the third quarter on Phil Dawson’s 46-yard field goal. Dawson extended the lead to 26-21 with a 31-yard field goal with 6:35 remaining.
KAP SHOWS OFF ARM: The 49ers took a lead on the first play of the second quarter on a play that demonstrated Kaepernick’s unique arm strength.
Kaepernick rolled to his left and was just outside the numbers when he threw across his body to just inside the numbers on the right side. The throw traveled 14 yards down the field and 30 yards across the field to running back Frank Gore, who caught the pass and ran the final 43 yards for a 55-yard touchdown.
INJURY CONCERNS: Vernon Davis and Anthony Davis returned from injuries to start Sunday’s game only to leave early with different physical problems.
Right tackle Anthony Davis made his season debut, but it did not last long against the Philadelphia Eagles. He returned to the starting lineup just long enough to sustain a left knee injury when he got rolled up from behind in the second quarter.
After leaving the field under his own power to go to the locker room for further observation, it was determined Davis could not return to action.
The extent of his knee injury was not immediately known.
Tight end Vernon Davis caught a 5-yard pass early in the third quarter and sustained an injury to his lower back on his left side. He walked slowly back to the locker room, and was immediately ruled out.
Anthony Davis missed the first three games of the regular season with a hamstring strain. Vernon Davis sat out last week’s game against the Arizona Cardinals due to an ankle injury he sustained Sept. 14 against the Chicago Bears.
JOHNSON TIGHT-ROPE ACT: Wide receiver Stevie Johnson helped pull the 49ers to within one point in the middle of the third quarter with a 12-yard touchdown catch from Kaepernick.
Johnson matched to catch the ball away from his body with Eagles cornerback Cary Williams in tight coverage while managing to get both feet inbounds in the left front corner of the end zone.
The 49ers’ defense set up that touchdown with Antoine Bethea’s strip of Philadelphia tight end Zach Ertz that was coupled with Cox’s recovery inbounds at the 23-yard line.
THIS ‘N’ THAT
--Bethea made his 100th consecutive start and registered the 15th interception of his nine-year career. Bethea made the interception of a deep pass from Foles, whom Justin Smith hit as he was throwing late in the third quarter.
--Rookie Aaron Lynch replaced second-year outside linebacker Corey Lemonier as the team’s designated pass-rusher in nickel situations. Lemonier has been largely ineffective, as the 49ers try to compensate for the loss of Aldon Smith.
--Defensive lineman Tank Carradine, a second-round pick in 2013, was among the 49ers’ seven inactive players for the third time in four games this season.
--Dawson made field goals of 29 and 51 yards in the first half, as the 49ers trailed 21-13 at the intermission.
--Safety Eric Reid sustained a left hamstring strain while covering a play in which Eagles return man Darren Sproles returned an Andy Lee punt 82 yards for a touchdown to give Philadelphia a 21-10 lead. Reid remained in the game.
--The 49ers had a scare in the first quarter when wide receiver Michael Crabtree left the game with a left foot injury. Crabtree has experienced left foot fractures after his final season at Texas Tech and in the 2011 offseason with the 49ers. After being evaluated in the 49ers’ locker room, Crabtree returned to action wearing a different pair of shoes.