Stung by the blowout loss at Seattle, and hampered by injuries at key positions, the Niners never found a way to tame Indianapolis. They

flailed in the passing game, committed ill-timed penalties and seemed to wilt in the late stages — again. They have been outscored 31-0 in the fourth quarter over the past two weeks.

San Francisco trailed just 13-7 when the Colts got the ball with 11:14 left in the game, but it was the beginning of the end. Indy mounted a crushing 11-play, 80-yard drive, sustained by two defensive penalties on pass plays, and second-year quarterback Andrew Luck finished it with a perfectly executed bootleg off of a run fake; he strolled into the end zone and gave the Colts a 20-7 lead.

Trying desperately to mount some kind of attack, the 49ers instead handed the ball back to Indianapolis on a fumble in the pocket by quarterback Colin Kaepernick. Indy's Kavell Conner recovered at the San Francisco 8, and Ahmad Bradshaw scored from a yard out three plays later to ice the game.

Luck, Harbaugh's former pupil down the road at Stanford, was predictably poised in his NFL Bay Area debut. He didn't throw a touchdown pass, but completed 18 of 27 passes for 164 yards and managed to avoid several sacks.

"I know he's grinning from ear to ear," Colts coach Chuck Pagano said of his quarterback. "I have never seen him smile the way he smiled after this win.

Compare that to the stony stare worn by Kaepernick after the game. Following a clunker against the Seahawks, he was nearly as bad against the Colts. Kaepernick completed 13 of 27 for 150 yards and threw an interception to punctuate the misery with 35 seconds left. He also ran for just 20 yards — 4 yards fewer than Luck, who isn't supposed to be nearly as mobile.

It must have felt like sweet revenge for Colts defensive coordinator Greg Manusky, who worked here under Mike Singletary.

Of course, Kaepernick was severely limited in his weaponry. Already missing wide receivers Michael Crabtree and Mario Manningham, both of whom have long-term injuries, the 49ers were without starting tight end Vernon Davis (who has a strained hamstring), perhaps their biggest mismatch on offense.

The fill-ins rarely got open against the Colts' press coverage. By halftime only one receiver, Anquan Boldin, had a reception. The numbers increased in the second half as the 49ers were forced to the air, but the efficiency did not. Guys like Kyle Williams, Marlon Moore and rookie tight end Vance McDonald simply couldn't separate from defenders consistently. Kaerpernick was forced to hold the ball, and he wound up sacked three times.

"As far as the defense is concerned, it's a huge threat off the field," McDonald said of Davis' injury. "Just in terms of having that safety net over the top for him bursting through, the linebackers. You just always have to be aware of him on the field. But that's not to say the next man isn't capable of filling in."

The San Francisco defense developed its own holes during the game, with star linebacker Patrick Willis (groin) and third cornerback Nnamdi Asomugha (knee) both leaving in the second half.

The injury excuse goes only so far, though. The Colts were missing three starters of their own, including Mike linebacker Pat Angerer and hard-hitting safety LaRon Landry on defense. They made better adjustments, and played with more intensity.

"It felt flat. It felt flat, looked flat," 49ers cornerback Tarell Brown said. "Guys have to come out with a lot more — and me included — we all have to come out with a lot more intensity. Start fast. We haven't started fast all year, and we're used to starting fast."

The Niners don't have long to get the fire lit. The Rams are just 1-2, but played the 49ers tough a year ago, tying here and winning in overtime in St. Louis.

Asked whether he was confident his team could find its way after consecutive setbacks, Harbaugh answered: "Yes. We have no choice. No choice but to find our way."

<i>You can reach Staff Writer Phil Barber at 521-5263 or phil.barber@pressdemocrat.com.</i>