NEW ORLEANS – Colin Kaepernick ran for one score that he made look easy and threw for a touchdown in another performance that validated coach Jim Harbaughs decision to start him.
The San Francisco defense added its share of big plays and the 49ers ended the New Orleans Saints three-game winning streak, 31-21 on Sunday.
Ahmad Brooks and Donte Whitner each returned interceptions for touchdowns and the 49ers sacked Brees five times.
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. 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.
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 with the club.
The Niners gained 144 yards on the ground, led by Gore with 83. The Saints shut down tight end Vernon Davis, the player they feared perhaps the most, but the Niners other tight end, Delanie Walker, had three catches for 81 yards, including one for 45 yards to set up a touchdown.
San Franciscos interceptions came during a 21-0 spurt that turned a 14-7 deficit into a 28-14 lead.
Brooks snagged the first, returning it 50 yards late in the first half. The second came on Brees first pass of the second half. The ball deflected off Colstons 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.
Brooks, Aldon Smith and Justin Smith each had 1 1/2 sacks, all in the second half.
Since losing to the New York Giants on Oct. 14, the Niners are 5-0-1 and now hold a 2 1/2 -game lead in the NFC West with five games to go.
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 this season before his injury.
The Saints, meanwhile, missed a chance to pull into a tie for the last NFC wild card berth, and remain a game out.