The one bit of good news: the game didn't count.
''It's something that's definitely a rude awakening for this team,'' Gates said. ''I'm glad it happened. It's one of those things that happens and you're upset, but it could be a positive thing.''
That would be one of the few positives.
Rivers went 8 for 10 for 89 yards and the interception in one quarter for San Diego, which will be back in the Bay Area to open the season on Monday Night Football Sept. 10 at Oakland. Rivers also tried to dodge another mistake, but San Francisco 49ers coach Jim Harbaugh had none of that.
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.
''The biggest thing that we've got to do is whoever has the ball, when the play is over, we end up with it,'' Chargers coach Norv Turned quipped.
QB Philip Rivers
Kyle Terada/US Presswire
Delanie Walker caught a 32-yard touchdown pass from backup quarterback Colin Kaepernick and starter Alex Smith handed off five times before calling it a night. San Francisco also wrapped up the preseason 3-1.
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.''
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 - particularly the backups - after 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.
Not that San Diego did enough right on offense to give the No. 2 defense 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.
Gates caught a 13-yard pass from Rivers, was stripped by 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.
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 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,'' Gates said, ''not what we worked this hard for.''
What did you think about Thursday's game? Talk about it inside the message boards.