SAN FRANCISCO -- It was a surprise to many that linebacker Aldon Smith played in the 49ers' 27-7 loss to the Indianapolis Colts on Sunday. But moments after the game concluded, 49ers CEO Jed York announced that Smith would be taking an indefinite leave to seek substance abuse treatment and won't be joining the team on its trip to St. Louis to face the NFC West rival Rams on Thursday night.

Smith started Sunday's game despite being arrested a little more than 48 hours earlier on suspicion of drunken driving. How long he could be out or what penalties still might be pending with the NFL were not immediately known.

Smith and York addressed the media at Candlestick Park, with Smith issuing a brief statement in which he apologized to the 49ers and his family for letting them down and admitted that he has a "problem."

"It's something I will get fixed," Smith said, while standing before a media crowd in front of his locker. "I'll do everything in my power to make sure this never happens again."

Smith did not field any questions. A minute or so later, York stood before the media.

"In talking with Aldon and knowing what he wants to do, there's not a one-day fix," York said. "This is a long-term fix. We support Aldon, and Aldon's willing to fight for himself and try to make this right."

Smith reportedly had a blood-alcohol level of 0.15 percent, or nearly twice the legal limit of 0.08, when he crashed into a tree in front of a house in San Jose on Friday morning.

Sports Illustrated's Peter King said Sunday that Smith will enter an inpatient facility early next week. York refused to divulge specifics of Smith's intentions during his leave.

The 49ers came under fire when they allowed Smith to practice Friday afternoon, a short time after Smith posted bail and was released from jail. They also got criticized for allowing Smith to play Sunday.

Former NFL coach Tony Dungy, a commentator on NBC's "Sunday Night Football" telecasts, was asked if he would have played Smith.

"I would not have. Number one, to help Aldon Smith, and get him some help right away. Number two, send a message to your team," Dungy said. "We're not going to have these types of incidents on a Friday before a game. I think Jim Harbaugh could have sent a stronger message."

Defensive tackle Ray McDonald said he had no qualms with the 49ers' decision to let Smith play and defended Smith's character.

"I know Aldon as a teammate and a friend," McDonald said. "He's a great guy. Sometimes things happen in life. People make mistakes. People want to come down on him because he's one of the best in the league. They need to look in the mirror, because we're all human and all make mistakes."

Coach Jim Harbaugh said Smith played Sunday because "it's a decision we made."

Strong safety Donte Whitner said Smith playing Sunday didn't pose a distraction.

"I don't think guys were out there thinking about Aldon (Smith) getting arrested," Whitner said.

Now the 49ers face the prospect of playing the Rams without Smith and inside linebacker Patrick Willis, who suffered a groin injury Sunday.

York said he understands that the 49ers, York, general manager Trent Baalke and Harbaugh are going to take heat for the way they handled the situation.

"I will stand here and I will take any shots that anybody wants to write (about) the organization," York said.

Ultimately, the 49ers say they acted in a manner that they felt was in the best interests of Smith.

"As an organization, we talked to him," York said. "We feel like, again, there was no right decision, there was no right way to do it. But this was in our opinion the best way to do it."

York said he and others in the organization believed it was best for everyone involved that Smith faced the media and his teammates.

In addition, "paying him to sit when he's going to seek treatment in the future" didn't make sense, York said.

Smith played the entire game. He finished with five tackles, but no sacks, as the 49ers lost their second straight game.