SAN FRANCISCO -- On a morose afternoon that ended with team officials defending a controversial decision to play an embattled Aldon Smith, the 49ers were overall left stunned by a second straight defeat.

Sunday's 27-7 loss to the Indianapolis Colts reinforced many of the 49ers' ills, which they'll now attempt to remedy without their reigning team MVP.

Smith, arguably the league's premier sack artist, is taking an indefinite leave of absence to seek treatment as a result of Friday's arrest on suspicion of drunken driving, his second such arrest since January 2012.

Team CEO Jed York said Smith will not play in Thursday's game at St. Louis, where the 49ers will try to snap their first two-game losing streak since coach Jim Harbaugh took over in 2011.

Smith offered a widespread apology in a prepared statement, adding: "I also want to let it be known that this is a problem. It's something I will get fixed. I'll do everything in my power to make sure this never happens again."

On the field, the 49ers (1-2) repeated their downfalls from last week's 29-3 loss in Seattle: a stagnant offense, costly penalties, numerous injuries and an eventual defensive collapse.

Smith, who still faces a potential suspension by the league, didn't add to his team-high 31/2 sacks. That wasn't the root of the 49ers' evils.

The 49ers offense looked nothing like the one that blistered the Green Bay Packers two weeks earlier in a triumphant opener at Candlestick Park.

"We ain't having no drives, making those big plays, too many three-and-outs (and) we're not getting in rhythm," running back Frank Gore said.

Gore and the 49ers' once-powerful rushing attack looked back on track while keying their lone touchdown drive, a 91-yard, game-tying march in the first quarter that Kendall Hunter capped with a 13-yard touchdown run on a draw.

But Gore had just three carries for 12 yards after halftime, and the 49ers couldn't generate offense elsewhere, most noticeably among an inept receiving corps that sorely missed tight end Vernon Davis, who sat with a hamstring injury.

Quarterback Colin Kaepernick put up similar passing numbers to his Seattle shortcoming: 13 of 27 for 150 yards with one interception and three sacks. A week earlier, he was 13 of 28 for 127 yards with three interceptions and three sacks.

"I have to be able to throw receivers open and give them a chance to make plays," Kaepernick said.

For the 11th time in Kaepernick's 13 starts, the 49ers failed to produce a first down on their opening series. Defensively, the 49ers weren't any better, allowing Stanford product Andrew Luck to lead an 80-yard touchdown drive on the game's first series, ending with a 1-yard scoring run from newcomer Trent Richardson.

"I thought our team was ready to play 100 percent," Harbaugh said.

Cornerback Tarell Brown said otherwise: "Felt flat, looked flat. Guys have to come with a lot more intensity and start fast. We haven't started fast all year."

By the time Luck scored on a 6-yard bootleg with 4:13 remaining, there was little doubt the Colts (2-1) had secured an upset of an increasingly wounded 49ers squad.

Headlining Sunday's injury report was star linebacker Patrick Willis, who left late in the third quarter with a groin injury that could keep him out of Thursday's game. Also exiting were special-teams ace Bubba Ventrone (concussion) and cornerback Nnamdi Asomugha (right leg).

Harbaugh said he had no insight into the severity of Willis' injury. As for the rest of the 49ers' problems, Harbaugh said: "We didn't make the plays. There wasn't enough opportunity to make plays."

Smith had his chances, playing almost every defensive snap while Justin Smith and Ray McDonald got more relief. So why did Aldon Smith play in the first place?

"It was the decision that we made as an organization, as a team, that we felt was in the best interest of our team and for Aldon long term," Harbaugh responded.

While Smith made five tackles, the defense overall allowed more rushing yards (179) than Luck passing yards (164).

"We knew if we could run the ball and stop the run -- that is what Coach (Chuck) Pagano preaches -- then we would have a fighting chance," Luck said.

The 49ers have 13 rounds left in defense of their NFC title belt. Can they get off the mat after back-to-back knockouts?

For more on the 49ers, see Cam Inman's Hot Read blog at blogs.mercurynews.com/49ers.

THURSDAY'S GAME
49ers (1-2) at St. Louis (1-2), 5:25 p.m. NFL Network, KGO

INSIDE
  • Aldon Smith taking indefinite leave from 49ers. page 4
  • S.F. offense nowhere to be found, writes Mark Purdy. PAGE 5