SAN FRANCISCO — Outside linebacker Aldon Smith played virtually every defensive snap for the 49ers on Sunday. His toughest assignment may have come after the game, when he stood in front of his locker and delivered the following message to a phalanx of reporters:

"First off I wanted to apologize to the team, the organization, my family and everybody I let down. I also wanted to let it be known that this is a problem and it's something that I will get fixed, and that I'll do everything in my power to make sure that this never happens again."

Smith did not field questions, but a little while later 49ers CEO Jed York confirmed rumors that had been swirling throughout the day. The star pass rusher will be removed from the team for a while — the 49ers did not call it a suspension, saying that Smith will "take an indefinite leave" — in the wake of his DUI arrest in San Jose early Friday. News outlets were reporting that Smith would enter a drug-and-alcohol rehab facility.

York said there is no timetable on Smith's return, though he said the linebacker will miss Thursday's game at St. Louis.

"This is a long-term fix," York said. "We support Aldon if Aldon is willing to fight for himself and try to make this right<NO1>, and I will stand here and I will support him and I'll take any shots that anybody wants to direct at the organization. You can direct them to me."

The 49ers took heavy flak after deciding to let Smith play Sunday. This is his second DUI since coming to San Francisco in the 2011 draft, and he was also stabbed during a party at his house last offseason. Police found Smith behind the wheel of his car at 7 a.m. Friday, his engine running and the front end of his vehicle smashed into a tree.

Last year, the 49ers left defensive lineman Demarcus Dobbs home when the team traveled to St. Louis, following his arrest for DUI and marijuana charges. Double standard or not, Smith played extensively Sunday, making little impact in the first half but finishing with five tackles. The Niners' defense will definitely suffer without him.

"It's a big loss, if that's the case," cornerback Tarell Brown said. "I don't really know. I don't really watch the news or things of that sort. That's ya'll job. But it would be a big loss for us."

<b>Foul play in the secondary</b>

The first two times the ball was snapped on Sunday, 49ers defenders were penalized. How fitting. Of San Francisco's six infractions against the Colts, five came against the defense on pass plays — and they did some damage.

Donte Whitner's unnecessary-roughness penalty (questionable though it was) and Tarell Brown's pass-interference call on Indianapolis' first possession helped propel the Colts to a touchdown. Brown's holding penalty in the second quarter negated a third-down stop and contributed to a field goal that gave the Colts a 10-7 lead. And in the fourth quarter, Indy's big touchdown drive was fueled by another PI on Brown and a defensive-holding call on which the offender was never identified.

"Yeah, it was a rough day," Brown said. "I think nine times out of 10 I would have got those calls, or they would have gone my way. But I guess the referee saw something different. It happens. I'm going to play aggressive. I'm not going to change my style of play."

<b>New guy makes some noise</b>

The Colts traded for Trent Richardson on Wednesday. He showed up at the team's facility on Thursday. But the running back's lack of familiarity with the Indianapolis playbook didn't force him to the sidelines.

Richardson's first carry as a Colt resulted in the team's first touchdown Sunday. He finished with 35 yards on 13 carries and was targeted three times in the passing game, though he didn't catch any of them.

"I hit the playbook real hard and got to studying," Richardson said. " .<TH>.<TH>. I just had to let the game come to me. Also, Andrew Luck is a genius and (running back) Ahmad Bradshaw helped me out."

Bradshaw finished with 95 yards on 19 rushing attempts.

<b>Still a great quote</b>

Former 49ers defensive tackle Ricky Jean-Francois, now with the Colts, on his new team's 27-7 victory: "We knew it was going to be a Frazier-Ali fight. But we had to make sure we got the last punch in."

<b>Extra points</b>

= LB Patrick Willis, who strained his groin against the Colts, is not expected to play against the Rams on Thursday.

= This is the first time a Jim Harbaugh team has had a losing record, at any point of the season, since his Stanford Cardinal squad finished 5-7 in 2008.

= With 21 receiving yards, Frank Gore passed Hugh McIlhenny and moved into second place among all 49ers running backs with 2,687 for his career. Roger Craig holds the franchise record with 4,442 receiving yards.

= The 49ers have surrendered 351 rushing yards in their past two games. That's the most in back-to-back games since they gave up 226 to Buffalo and 174 to New England in the final two weeks of the 2004 season.

= TE Vance McDonald made his first career start, and DT Glenn Dorsey made his first with the 49ers.

= Former Raiders Darrius Heyward-Bey had 59 yards on five receptions for Indianapolis.