NEW ORLEANS -- Colin Kaepernick took another victorious step as the 49ers' starting quarterback Sunday. But the 49ers defense stole the show for how it treated Kaepernick's heralded counterpart, New Orleans Saints star Drew Brees.
Ahmad Brooks and Donte Whitner intercepted back-to-back throws by Brees to spark the 49ers' 31-21, come-from-behind win inside an ever-imposing Superdome.
"Big plays by the defense really swung the game for us," 49ers coach Jim Harbaugh said.
Added Brees: "Unfortunately, it's the turnovers in the end that did us in."
Those defensive touchdowns came in the second and third quarters, and they were sandwiched around an expedited 49ers series that produced a go-ahead touchdown pass from Kaepernick to Frank Gore.
Despite Kaepernick's play-making thrills in his second straight start, Harbaugh declined to deem Kaepernick an entrenched successor to Alex Smith, who was medically cleared Saturday from a Nov. 11 concussion and suited up as an idle backup.
What Harbaugh did reinforce was how well the 49ers battled to go unbeaten for a fifth straight game. They'll take an 8-2-1 record up the Mississippi River next Sunday for a visit to the St. Louis Rams (4-6-1).
Defeating Brees & Co. inside their noisy dome was a mighty task, and one that got accomplished in familiar ways. The 49ers' pass rush produced all five of its sacks after halftime, and their run defense yielded a mere 59 yards. The greatest wallops, however, came from the "pick-six" efforts of Brooks and Whitner.
Brooks' 50-yard return for a touchdown rescued the 49ers from first-half sorrows, and it tied the score at 14-14 with only 22 seconds left before halftime.
"When an opportunity presents itself, you've got to make a play," Brooks said of his second career interception. "Unfortunately, I didn't do that against St. Louis, and I could have ended the game that way."
Although Brooks couldn't corral an overtime pass in the Nov. 11 tie against the Rams, Brees credited Brooks for making "an extremely athletic play" to snare a pass intended for tight end Jimmy Graham.
Brooks went untouched into the end zone, and although Brees gave pursuit, "he wasn't going to catch me," Brooks insisted.
That return inspired Whitner to find the same end zone after he snatched Brees' pass, which went off Marques Colston's hands as he got hit low by safety Dashon Goldson.
"I've dropped two or three this year, and when I caught this one, I made it worth my while," Whitner said of his 42-yard return.
With a 28-14 lead, the 49ers defense kept up its hard-hitting ways against a Saints team desperate to stay in the playoff hunt after having won five of its past six games. Brooks, Aldon Smith and Justin Smith each registered 1½ sacks, and that pushed Aldon Smith's league-leading total to 16½.
Kaepernick did a phenomenal job not getting sacked once. He scrambled out of danger and often found a receiver to move the chains.
On the 49ers' final scoring drive, Kaepernick converted all three of his third-down passes, including a 25-yard rocket to tight end Delanie Walker. On the down side, Walker apparently injured his hip on the play and had to be carted to the team bus after the game.
That scoring drive chewed up 9½ minutes and ended with a 27-yard field goal by David Akers.
From there, the 49ers protected that lead by harassing Brees, who had been sacked only 16 times in the first 10 games. Brees finished 26 of 41 for 267 yards with three touchdowns and the two interceptions.
Kaepernick was 16 of 25 for 231 yards with a touchdown and a first-career interception. (Brooks' interception came two snaps after Kaepernick's off-target pass.)
Coming off a dazzling starting debut last Monday against the Bears, Kaepernick put the 49ers ahead 7-0 midway through the first quarter by running for his fourth touchdown of the season, via a 7-yard, read-option keeper. Kaepernick dashed between blocks from Randy Moss and Bruce Miller, and Kaepernick then crossed the goal line untouched with the ball raised high in his right hand.
Kaepernick was congratulated on the 49ers sideline with a brief hug from Harbaugh and an approving tap to the helmet by Smith, who praised Kaepernick's showing but also said he wants to reclaim his starting job.
While that quarterback drama continues, it hasn't appeared to distract the 49ers defense. "We know we gave up some yards," linebacker Patrick Willis said, "but when it counted, our defense held together and won the game for us."