NEW ORLEANS Colin Kaepernick had one more touchdown pass than rival Drew Brees on Sunday, but for the second straight game finished with meager passing yards and had none of his 2012 magic at the end of the game.
Kaepernick seemed to be at his best when rolling to his right out of the pocket. He connected with Vernon Davis on a 17-yard touchdown pass early in the third quarter when doing so, and he hit Anquan Boldin twice to his right on a 13-play drive in the fourth quarter that ended with a Phil Dawson 29-yard field goal.
But when the 49ers had the ball with 2:06 remaining and the game tied at 20, Kaepernick was stuck in the pocket. He was sacked for a nine-yard loss on first down, had to throw the ball away and narrowly avoided a safety on second down and scrambled for 16 yards on third down before running out of bounds three yards short of the first-down marker.
Afterward Kaepernick said he was trying to pick up the first down. But running out of bounds stopped the clock, allowing the Saints to preserve their lone remaining time out for their final, game-winning drive.
Kaepernick, who had 91 passing yards in last weeks loss to Carolina, finished with 127 yards against the Saints. He completed 17 of 31 passes, and his longest completion of the day was the 17-yard touchdown toss to Davis.
He had a chance for a much longer play midway through the fourth quarter.
Kaepernick scrambled to his left away from pressure and flipped the ball to Frank Gore who had great swaths of running room in front of him. Gore, however, could not make the catch at his ankles, and on third down Kaepernicks pass to Jon Baldwin fell incomplete.
I thought Colin played very well, very accurate, Jim Harbaugh said. He was fighting, just like everybody. Very aggressive, a lot of big-time throws ...
Red-flag blues Harbaugh was 0-2 on replay challenges in the first half, causing the 49ers to burn through all of their timeouts with more than 10 minutes remaining in the game. He said he confers with offensive consultant Eric Mangini, who is in the coaches booth, on challenges.
Both turned out to be bad decisions. On the first, Harbaugh argued that Brees had crossed the line of scrimmage before tossing a short pass to running back Darren Sproles. Replays showed Brees entire body was behind the line of scrimmage as he completed the throw.
Harbaugh said the 49ers never saw a replay of that particular play but decided to challenge it anyway.
Harbaugh later challenged whether Baldwin had lost control of the ball on his way to the ground after a pass attempt in the end zone. Replays upheld the ruling on the field on that play, too.
Iupati injured Mike Iupati left the Superdome on crutches and with a brace around his left knee after being injured in the third quarter. The injury appeared to occur when Gore crashed into the big guards knee on a run for no gain, and Adam Snyder filled in at left guard for the rest of the game.
Iupati also went down last week against Carolina but was able to return to the game. The 49ers offensive line has been remarkably resilient since last season. The same five members started every game in 2012 as well as the first 10 games this season.
Snyder and third-year player Daniel Kilgore are options to start next week against Washington if Iupati is unable to play.
Meanwhile, starting cornerback Tarrell Brown suffered a rib injury in the second quarter and was in obvious pain as he exited the locker room. His absence meant more snaps for Tramaine Brock and for Eric Wright, who was in uniform for the first time this season.
Wright said he prepared for the game thinking he would play on the inside in the team's nickel- or dime-defense packages. Instead, he played nearly the entire second half outside at left cornerback.
He finished with four tackles but also gave up a 26-yard pass to Marques Colston in the fourth quarter.
Read Matthew Barrows blogs at www.sacbee.com/sf49ers and listen for his reports Tuesdays on ESPN Radio 1320.