SAN DIEGO -- Colin Kaepernick safely closed out his 40-snap exhibition season, eliminating any pressing need for whoever ends up as the 49ers' backup quarterbacks.

But when it comes to the 49ers, the quarterback position is historically a hot-button topic, and Thursday was no different en route to a 41-6 rout of the San Diego Chargers.

Seneca Wallace bowed out of the No. 3 quarterback race Thursday morning when he told the 49ers he had ended his comeback attempt, according to general manager Trent Baalke and coach Jim Harbaugh.

"Yeah, that was a surprise," Harbaugh said. "It was his decision. He felt strongly about it, and I don't talk guys out of it. I've never seen it done on game day, but I wish him well."

Signed only a week ago, Wallace thus left the No. 3 spot unchallenged for rookie B.J. Daniels, who impressed in relief for a third straight game.

The 49ers have kept three quarterbacks in each of Harbaugh's two seasons as coach. They must trim their roster from 75 to 53 by 3 p.m. Saturday, and they were weighing how to term Wallace's transaction, as a retirement or a terminated contract.

More pertinent to the 49ers' quarterback cause, Kaepernick played sparingly all exhibition season, and he's fully healthy heading into his first full season as their starter.

"I'm very relieved and feel very good," Harbaugh said about Kaepernick's and the team's overall ability to avoid exhibition-season injuries.

Kaepernick made a one-series cameo Thursday -- as was the case in the first two exhibitions -- and exited after Quinton Patton's 43-yard, catch-and-run touchdown for a 7-0 lead.

Kaepernick wasn't sacked in any of his six exhibition series, and he finished 15 of 23 for 171 yards, with two touchdown passes, no interceptions and a 116.4 passer rating.

"I don't know how much momentum you get from the preseason, but I think we're ready to focus on Green Bay," Kaepernick said of the 49ers' opening-day opponent Sept. 8 at Candlestick Park.

Settling on Kaepernick's backups looked like a convoluted situation a week ago, when Wallace's addition gave the 49ers a five-man quarterback crew, at least until Scott Tolzien was waived Monday.

Cut last week by the New Orleans Saints, Wallace figured to challenge Colt McCoy as a veteran option. But McCoy restructured his contract Saturday night and was named the No. 2 quarterback by Harbaugh after Sunday's rout of Minnesota.

McCoy replaced Kaepernick after one series Thursday night and played into the third quarter. McCoy finished 8 of 15 for 56 yards with a 5-yard touchdown pass to Anthony Dixon. He had no passes intercepted for the first time in four games, and he ran four times for 12 yards.

Daniels failed to produce a first down in his first three series. But after scrambling for a first down and losing his helmet in the process, Daniels connected with Lavelle Hawkins for a 45-yard touchdown reception and a 34-6 lead. Daniels later had a 36-yard scramble, setting up a 5-yard touchdown on a fade to Chuck Jacobs, his target for a go-ahead touchdown two weeks ago in Kansas City.

  • Outside linebacker Cam Johnson helped his cause, producing two sacks before halftime and then blocking a third-quarter punt that he recovered in the end zone for a touchdown.

    "I know I don't have a solid spot on the roster," Johnson said. "I've been working all offseason to get one. I'm just happy to finally see positive things, and I hope for more."

    Two days after trading Parys Haralson, the 49ers also got first-half sacks from their other backups at outside linebacker: Dan Skuta and Corey Lemonier.

    Asked if the 49ers could keep five outside linebackers, Harbaugh enthusiastically replied: "After tonight, the way Cam Johnson played, heck yeah, we can. We're the San Francisco 49ers. We can do whatever we want!"

  • Patton, starting in place of Anquan Boldin, impressed beyond his second touchdown catch in two games. He also had a 9-yard catch and averaged 34.5 yards on two kickoff returns, both of which he fielded deep in the end zone.

  • All of the 49ers' projected Week 1 defensive starters -- and No. 3 cornerback Nnamdi Asomugha -- got the night off except for nose tackle Ian Williams. The rest of the makeshift lineup: Lemonier, Skuta, Will Tukuafu, Demarcus Dobbs, Nick Moody, Michael Wilhoite, Tramaine Brock, Perrish Cox, Craig Dahl and Trenton Robinson.

  • Kevin McDermott handled all the long-snapper duties while Brian Jennings sat out.

  • On Hawkins' touchdown catch, he tipped Daniels' pass in the air to himself and then bounced off safety Jahleel Addae's hit at the 33-yard line. "Highlight play, spectacular play," Harbaugh said.

    SEPT. 8 OPENER
    Green Bay at 49ers, 1:25 p.m. Fox