With the 49ers' defense making big plays of its own, it might not have mattered who was under center.
Ahmad Brooks and Donte Whitner each returned interceptions for touchdowns, a pass rush led by Aldon Smith sacked Drew Brees five times, and San Francisco ended New Orleans' three-game winning streak, 31-21 on Sunday.
"We always want to be the best defense on the field, especially on the road," Whitner said. "When you play us, you are going to get hit. That's our identity: smart, hard-nose, physical football."
Kaepernick was solid in his second career start while Alex Smith, deemed healthy enough to suit up after recovering from a concussion, watched from the sideline in uniform. Kaepernick passed for 231 yards, including a short touchdown to Frank Gore. He also ran for a 7-yard score. He threw his first career interception, but it was inconsequential.
"We got a win, so that's all that really matters," Kaepernick said.
Niners coach Jim Harbaugh implied the decision to start Kaepernick had more to do with preserving Smith's long-term health than on performance, but he was noncommittal about who might start next week at St. Louis.
"The fact he had symptoms seven to eight days later, I'm not going to put a guy back out there," Harbaugh said of Smith. "He eventually got cleared. The plan was to rotate him back into the action (in practice), but not all the way to the front line. ... That would give him a chance to get cleared up completely."
Smith did not seem to think he needed to more time, but kept complaints to a minimum.
"Obviously I want to play. I want to start. I think I should, but it's not my decision," Smith said. "I'm part of this team and it's great to go out and get a win."
Brees finished with 267 yards and three TDs. After rushing for 140 yards or more in each of its previous three games, New Orleans (5-6) managed only 59 yards against San Francisco (8-2-1).
One of Brees' scoring passes went to Marques Colston, who set a Saints record with his 56th career touchdown for the club.
The Niners gained 144 yards on the ground, led by Gore with 83. The Saints shut down tight end Vernon Davis, but the Niners' other tight end, Delanie Walker, had three catches for 81 yards, including one for 45 yards to set up a touchdown.
The Saints had to play recently acquired reserve William Robinson at right tackle after rookie Bryce Harris, making his first start because of injuries to Zach Strief and Charles Brown, was carted off with an apparent right leg injury. But just about every Saints lineman was beaten on a Niners sack. Brooks, Aldon Smith and Justin Smith each had 1 1/2 sacks, all in the second half.
"They're a good defense," Saints assistant head coach Joe Vitt said of San Francisco. "When you lose your right tackle and you've got to play with a young man who's been here four days, that's a tough challenge."
San Francisco's interceptions came during a 21-0 spurt that turned a 14-7 deficit into a 28-14 lead.
"You give them two free ones and that's what they thrive on," Brees said. "All of a sudden they rattle off 21 points in a short amount of time and we really felt like we had the game under control."
Brooks snagged the first, returning it 50 yards late in the first half to tie the game at 14.
The second came on Brees' first pass of the second half. The ball deflected off Colston's hands as the leaping receiver was upended and briefly shaken up. Whitner snagged the deflected pass and returned it 42 yards to make it 28-14.
Since losing to the New York Giants on Oct. 14, the Niners are 5-0-1 and hold a 2 1/2-game lead in the NFC West.
It seems their biggest problem at this point is deciding who should be their No. 1 QB. Smith, who led the Niners to the NFC title game last season, started the first nine games.
"That would be coach's decision," Kaepernick said. "I'm just trying to take a similar approach that I've been taking, just keep my head down, keep working and see where it takes me."
The Saints, meanwhile, missed a chance to pull into a tie for the last NFC wild card berth, and remain a game out with another tough game coming up at Atlanta on Thursday night.
Kaepernick gave the Niners the early lead, scoring easily on a read-option run that fooled the Saints' defense.
New Orleans tied it on tight end David Thomas' 6-yard catch, then took the lead on Colston's TD, capping a drive that began when Ted Ginn Jr.'s fumbled punt was recovered by Rafael Bush on the 49ers 10.
New Orleans was looking to go up by two scores after Kaepernick's interception on an underthrown pass that cornerback Patrick Robinson easily caught. Instead, Brooks tied it, stepping in front of a pass for Jimmy Graham.
Saints DT Brodrick Bunkley was thrown out for unsportsmanlike conduct with 1:05 left for kicking lineman Alex Boone in the back of the helmet right after the Saints had blocked a field goal ... Aldon Smith's sack of Brees in the third quarter was his 16th this season, 30th in his career. He became only the second player to reach 30 sacks in his first two seasons, joining Reggie White (31) and Derrick Thomas (30). He reached it in fewer games (27) than either of them. ... Niners WR Kyle Williams and RB Kendall Hunter both were shaken up on the same play in the second half. ... Saints S Isa Abdul-Quddus left the game after a hard collision with tight end Delanie Walker in the fourth quarter.