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SAN FRANCISCO -- Jim Harbaugh wanted tight end Delanie Walker to play a bit more than the rest of San Francisco's starters in the final preseason game, considering a bum knee had limited him during training camp.

Walker caught a 32-yard touchdown pass from backup quarterback Colin Kaepernick, Alex Smith handed off five times before calling it a night and the 49ers wrapped up the preseason with a 35-3 win over the San Diego Chargers on Thursday.

Walker returned to action for the first time since the exhibition opener after he injured his right knee during practice Aug. 12. He missed time late last season with a broken left jaw before returning for the NFC championship, so the TD catch will only serve as a boost heading into the regular season next weekend.

"I missed two preseason games, so just the opportunity to go out there and play, I took advantage of it, and I had a great time," Walker said. "I wanted to get my feet back under me, make sure the knee was good. I felt like everything was perfect and had a great game."

Philip Rivers went 8-for-10 for 89 yards and an interception in one quarter for San Diego (3-1), which will be back in the Bay Area to open the season on "Monday Night Football" on Sept. 10 at Oakland.

Harbaugh hollered at the replacement officials when they didn't initially call intentional grounding on Rivers' left-handed throw under pressure with 3:10 remaining in the first quarter. Neither considered it a big deal afterward.

Kaepernick connected with rookie first-round draft pick A.J. Jenkins on a 12-yard score midway through the second quarter that put the defending NFC West champion ahead 21-0. Kaepernick finished 12-for-18 for 158 yards and two touchdowns for the 49ers (3-1).

"Tonight was the first time I really felt like I just went out there and let it loose and just played ball," Kaepernick said. "It felt good to finally get in a rhythm."

Smith didn't throw a pass in his short outing, handing the ball to Kendall Hunter on the first four plays of the game and one more to Jenkins. Anthony Dixon ran for a 1-yard TD.

"Just wanted him to go out and break a sweat," Harbaugh said.

San Francisco defensive coordinator Vic Fangio called out his unit's struggles -- particularly the backups -- in a 29-24 win at Denver on Sunday night in which the Niners fell behind 17-0 in the first quarter before rallying in the second half to win. This time, the 49ers' starters got the night off completely on a windy, chilly summer evening along the bay at Candlestick Park.

Not that San Diego did enough right on offense to give the No. 2 D much of a test.

San Francisco's Josh Johnson, fighting for the No. 3 quarterback job with 2011 holdover Scott Tolzien, threw a 51-yard touchdown pass to Nathan Palmer in the third quarter and another late in the period to Garrett Celek for 3 yards.

Walker's first-quarter touchdown catch -- and Kaepernick's first career TD completion as he begins his second season with San Francisco -- was set up by safety Trenton Robinson's 22-yard fumble return.

Antonio Gates caught a 13-yard pass from Rivers and was stripped by C.J. Spillman, and Robinson recovered and ran.

"I didn't realize how close he was to me," Gates said. "So when I caught the ball, he was right there. It was kind of a challenge for the ball at that point because I kind of carelessly, loosely, brought the catch in. I know better than that."

Two plays after the fumble, Walker caught the ball on a crossing route to the left sideline and beat safety Atari Bigby at the 5 before spinning into the end zone for the Niners, who went 13-3 last year in a resurgent season under Harbaugh, the NFL coach of the year.

"He was fired up about that play and made a tremendous athletic play," Harbaugh said.

Darcel McBath intercepted a pass by Rivers on San Diego's next possession. The Chargers are counting on Rivers to carry the franchise back to its old winning ways as a contender in the AFC West after two years out of the playoffs.

It gets much harder for Harbaugh's crew now.

San Francisco opens the season at Green Bay on Sept. 9 in a big test for two teams that consider themselves Super Bowl contenders.

The 49ers would rather not rely quite so heavily on All-Pro kicker David Akers and his NFL-record 44 field goals from 2011. Akers missed a 47-yarder wide right on the last play of the first half and went 8-for-9 in the preseason.

Nate Kaeding kicked a 27-yard field goal in the opening minute of the fourth quarter for San Diego's lone points.

"What was displayed today was not what we are about, not what we worked this hard for," Gates said.

Game notes

Harbaugh said LB Parys Haralson "is working through something," but declined to elaborate. ... San Francisco rookie RB LaMichael James muffed two punts and bobbled a third. ... 49ers LB Aldon Smith didn't play after all as Harbaugh had said he probably would. Smith, who had a 49ers rookie record 14 sacks in 2011, injured his right hip in the exhibition opener against Minnesota on Aug. 10. ... The teams must cut their rosters to the regular-season limit of 53 by Friday night. ... San Diego and San Francisco played in the preseason for the 26th straight year and 11 consecutive exhibition finales. San Francisco has won the past three. ... Tolzien threw an interception early in the fourth.