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New Orleans • Even if Colin Kaepernick's second start was hardly as spectacular as his first, he played well enough to extend coach Jim Harbaugh's quarterback quandary for at least another week.

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.

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.

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, the ex-Utah star. "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."

When asked about who might start next week, Kaepernick said, "That would be Coach's decision. 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."

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).

"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."

One of Brees' scoring passes went to Marques Colston, who set a Saints record with his 56th career touchdown for the club.

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 1½ sacks, all in the second half.

"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," Saints assistant head coach Joe Vitt said

San Francisco's picks 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." —

Monday's game

P Carolina at Philadelphia, 6:30 p.m.,ESPN