SAN FRANCISCO A 49ers running game that had been slumbering over the first two games seemed to wake up in the first quarter when Frank Gore broke off runs of 22 and 21 yards on the same possession.
The drive ended with Kendall Hunter taking a delayed handoff and scampering 13 yards to the right side of the end zone for a touchdown that tied the game 7-7.
But from that point on the running game, as well as the rest of the 49ers offense, returned to its previous sputtering state. San Francisco had 77 rushing yards on that drive alone but ended with only 115 ground yards for the day.
Gore finished with a season-high 82 yards but was clearly frustrated after the game.
"Well, when things aren't going right, you get frustrated," Gore said afterward in front of his locker. "But I think the game got kind of different in the second half, and we had to do what we had to do just throw the ball."
Asked if the 49ers should have continued with the running game, Jim Harbaugh said the goal was to stay balanced.
"And (we) did not have success moving the ball today or on third down," he said. "And couldn't make plays. Didn't find enough plays."
The 49ers were 3-12 25 percent on third-down conversions, the same rate they were last week in a blowout loss to Seattle.
Seeing yellow The 49ers entered the game tied for most penalties in the league, and they piled up a few more in the first half. The first two plays of the game, for example, were wiped away by an unnecessary roughness call against Donte Whitner the officials said he struck an opponent with the crown of his helmet and a pass-interference penalty on cornerback Tarell Brown.
Those penalties brought Indianapolis to near midfield. From there, Andrew Luck twice found his favorite target today, Darrius Heyward-Bey, before recently acquired tailback Trent Richardson walked into the end zone for a one-yard touchdown.
Brown was called for three penalties, two on a fourth-quarter drive that ended in a Luck touchdown run.
"You're taught to reach for the ball," Brown said. " It's a judgment call every time and the referees try to make the best call they can. Today they all went against me. I've never seen that happen before, but it does happen. But that's not going to change my play.
Injuries Linebacker Patrick Willis injured his groin in the third quarter Sunday and his availability for Thursday's game is in doubt. If he can't play, Michael Wilhoite would make his first career start.
Another defender, cornerback Nnamdi Asomugha, also left the game and was limping afterward. If Asomugha is out against the Rams, Tramaine Brock would serve as the team's No. 3 cornerback. Meanwhile, rookie Corey Lemonier is expected to start at outside linebacker in place of Aldon Smith, who is seeking treatment and will miss Thursday's game. Dan Skuta will be the only backup at outside linebacker.
Et cetera Hunter took over kick-return duties from cornerback Perrish Cox, who fumbled last week in Seattle. Hunter, however, struggled with a 14.5-yard average and was replaced late by rookie Quinton Patton, who bobbled a kickoff and returned it only seven yards.
Special teamer Ray Ventrone, who is the punter's personal protector, suffered a concussion in the first half and did not return. Craig Dahl took over Ventrone's duties while receiver Kassim Osgood filled in as a gunner on punt coverage.
Patton nearly had his first NFL catch on a third-down throw in the second quarter. He absorbed a big hit as the ball arrived, however, and couldn't hang on. The rookie remains catch-less.
Read Matthew Barrows' blogs at www.sacbee.com/sf49ers and listen for his reports Tuesdays on ESPN Radio 1320