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.

“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 with 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 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 1½ sacks, all in the second half.

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.”

NOTE: Niners receiver Kyle Williams and 
running back Kendall Hunter both were shaken up on the same play in the second half with apparent leg 
injuries.