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Drew Brees turned and sprinted toward his own end zone, trying in vain to chase down Ahmad Brooks.

One moment, Brees was looking to drive the Saints quickly for a two-score lead in the final minute before halftime. The next, he was watching Brooks return an interception 50 yards for a tying touchdown as the Superdome crowd gasped and groaned.

From there, it only got worse in a 31-21 loss to the 49ers on Sunday that snapped New Orleans' three-game winning streak and put a dent in the Saints' playoff hopes.

Donte Whitner also intercepted a pass by Brees for a score, and the Niners' pass rush led by Aldon Smith sacked Brees five times.

"Obviously, what was glaring were the two turnovers that resulted in touchdowns for them," Brees said. "That' can't happened, especially the first one right there at the end of the first half."

Colin 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.

The Saints had to play recently signed 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 one or more of the Niners' sacks. Brooks, Aldon Smith and Justin Smith each had 1½ sacks, all in the second half.

"They're a good defense. They've got a good front seven. They're physical," 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 quick 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 game under control."

The second interception 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.

The Saints 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.

"It's all right there in front of us," Brees said. "I firmly believe that if we take care of our business and worry about ourselves, we're going to have a chance at the end to get in" to the playoffs.

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.

NOTES: 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 with apparent leg injuries. ... Saints S Isa Abdul-Quddus left the game after a hard collision with tight end Delanie Walker in the fourth quarter.

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