Walker returned to action for the first time since the exhibition opener after he injured his right knee during practice on 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 passing 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 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.
"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."
"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.
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.
"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.
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.
They 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 passing 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.
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.
Copyright 2012 The Associated Press