Smith was arrested by police officers after a single-vehicle crash at approximately 7 a.m. PT in the city's Silver Creek district, San Jose police spokeswoman Sgt. Heather Randol told NFL Media. Smith's vehicle collided with a tree. Nobody else was in the vehicle when officers arrived, she said.
"The initial investigation revealed that he was driving under the influence of alcohol," Randol said.
Smith was taken to a Santa Clara County jail, where he was booked and later released on $5,250 bail, Sheriff's Office spokesman Sgt. Kurtis Stenderup said.
Smith also was booked on a charge of possession of marijuana, Stenderup said. Randol said there was no marijuana charge brought by San Jose police.
"I'm disappointed, and I felt like he needs to go to work, face his teammates and soldier through it," Harbaugh said.
"I expect Aldon, like today, he'll be back at work and playing on Sunday," Harbaugh said.
Smith, 23, previously was arrested for DUI in Miami Beach in 2012. In that case, Smith completed a program for first-time DUI offenders and got a lesser charge of reckless driving, said Ed Griffith, spokesman for the Miami-Dade State Attorney's Office.
Friday's incident marks the fifth 49ers-related DUI arrest in the last two and a half years, per Matt Barrows of The Sacramento Bee.
Smith also was recently named in a lawsuit filed by a man who claimed he was shot during a June 2012 party hosted by Smith at the player's San Jose area home. Smith reportedly was stabbed at the gathering.
Attorneys for Smith and former 49er Delanie Walker, who also is named in the suit, have said the man "freely and voluntarily exposed himself to all risks of harm" by attending the party, The Associated Press reported. The lawyers add that his injuries were not caused by the defendants.
A spokesman for the Santa Clara County Sheriff's Office told NFL Media on Friday the investigation into what happened at the party is ongoing.
The third-year defender has 3.5 sacks this season after piling up 19.5 takedowns in 2012.