SANTA CLARA, Calif. -- Chip Kelly didn't mince words after the 26-21 loss on Sunday at Levi's Stadium talking about his offense. "We got whupped up front," he said after the Eagles failed to score offensively against the 49ers. "That's not an excuse. That's just reality."

The Eagles manufactured just one offensive drive in the game and it happened to come late in the fourth quarter, and it took the Eagles all the way inside the San Francisco 10-yard line. Trailing by five points without mounting a thing offensively all day -- the Eagles scored on two special teams plays and a defensive touchdown -- quarterback Nick Foles and Co. moved the ball when they needed it most.

With six minutes, 26 seconds to go in the game, the Eagles started a drive at their 9-yard line. Not ideal, but that's the kind of day it was. The offense had no good field position, and had just five first downs to this point. But suddenly the offense got hot. Nick Foles went to Jeremy Maclin for 11 yards and a first down. A LeSean McCoy run gained five yards. Foles again found Maclin for 15 yards to the 40-yard line and two plays later connected with Maclin again for 11 yards to the San Francisco 49-yard line.

On first down from there, Foles completed a 14-yard pass to tight end Zach Ertz and you thought ... just maybe ...

On third-and-14 from the 35-yard line, Foles threw a pass toward the right sideline and Maclin made a diving, one-handed grab and landed in bounds for a first down at the 17-yard line, and two plays later Foles completed a throw to Jordan Matthews for 11 yards.

And here was the situation: First and goal from the 6-yard line. Four cracks at putting the ball in the end zone and taking a lead. On first down, Foles threw in the back of the end zone and Riley Cooper, in tight coverage, was unable to make the catch. Second down.

McCoy ran left and gained five yards to the 1-yard line to bring the game to the two-minute warning. Instead of trying to pound the ball on third down -- Kelly said the 49ers packed the line of scrimmage too much to try a running play -- Kelly called a pass and had tight end Brent Celek cross the formation from right to left in the end zone, and Foles just missed the veteran.

"Good coverage. It was a tough throw," said Celek. "We really felt good about that call and that play and it didn't happen for us."

On fourth down from the 1-yard line, Foles rolled right as tight end James Casey released toward the right pylon. He was covered. Foles looked into the middle of the end zone. Nothing there. A pass high into the back of the end zone was incomplete, and the threat was over.

"We need to score there," said Celek. "We just didn't do it. We'll go back and get it right, but we know that to have that opportunity, it's disappointing."

"We just didn't execute," said Foles. "It's as simple as that. I'm not going to try to break it down. In that situation, I've got to give the guys a chance to make a play and I didn't do that." 

The Eagles gained 90 yards on that drive, and only 123 on their other 10 drives. Six of the team's 11 first downs came on that nearly-golden drive. McCoy gained only 17 yards on 10 rushing attempts and the Eagles gained just 22 on 12 rushes.

The Eagles were in the game because they scored twice on special teams and once on a Malcolm Jenkins interception and sensational 53-yard return. They battled against a good 49ers team and came up short, and are now 3-1 on the season.

There was disappointment in the locker room afterward, but nobody hung his head. The Eagles know they are right there, and they know they are in good position at the quarter pole of the season.

"I think it's encouraging. I don't think that anybody looks at this game and lets it affect their confidence," said safety Malcolm Jenkins, who had an interception return for a touchdown, his third interception in the last three games. "The momentum squng in our direction early and they took it back and we couldn't finish. You're playing a good team on the road and you're one play away. We have that one play somewhere in this locker room. We just didn't make it today.

"That's encouraging to know that, no matter what, yet and still we're never out of a game. That's been our theme the last four weeks and we'll continue to have that."

Here are some takeaways from the loss, a tough one on the road ...

• The Eagles have to find a way to get the running game going, and maybe the return of right tackle on Lane Johnson this week will help. Nobody knows what kind of conditioning Johnson has had in the last month, but if he is able to step in and play, and the Eagles can move Todd Herremans back to right tackle, that would be a boost. Davidi Molk appeared to hold his own at center in his first start and Matt Tobin said he felt things went well in his first start at left guard. The Rams are next, with a tough front seven.

• Foles missed some receivers, but he also had very little cushion and time to set up and throw the football. He came so close to winning this game late with another fourth-quarter rally.

• The 49ers were all over Darren Sproles in the screen game. He had just 2 catches for 2 yards. The Eagles need to find a way to get him the ball in space.

• Special teams again delivered with the Sproles 82-yard punt return for a touchdown and the blocked punt by Trey Burton -- with an assist from Bryan Braman -- that was recovered by Brad Smith in the end zone.

• The defense battled, but a key defensive holding penalty against cornerback Cary Williams that wiiped out a Trent Cole sack on third and 15 kept a 49ers drive alive that ended with a Colin Kaepernick touchdown pass to Stevie Johnson that put San Francisco ahead, 23-21.

• San Francisco averaged 5.2 yards per rushing attempt and churned out 218 yards on the ground, completely dominating the time of possession and keeping the Eagles offense on the sidelines.

• Not a bad job rushing Kaepernick. The Eagles had 4 quarterback sacks. Kaepernick gained 58 yards on 7 rushing attempts and had a key 23-yard gain on a designed sweep right to convert a third down in the fourth quarter.

• There were no injuries reported from the game. Cornerback Brandon Boykins suffered a hamstring injury, but returned to the game.