Aldon Smith was arrested by officers who received a call about a solo vehicle crash around 7 a.m., San Jose police Sgt. Heather Randol said. Officers proceeded to take a breath sample and to conduct other tests.
"They conducted an investigation and determined he was under the influence," Randol said.
The team released a statement regarding the Pro Bowl linebacker Friday morning.
"The 49ers organization is aware of the matter involving Aldon Smith. As we continue to gather information regarding this situation, we will have no further comment," the team said.
Smith was booked into the Santa Clara County jail on $5, 250 bail where he remained in custody late Friday morning. It is not clear whether Smith will play Sunday for the Niners when they host the Indianapolis Colts at Candlestick Park.
The linebacker was also arrested on suspicion of drunken driving in Miami Beach in January 2012.
Smith has also been named in a lawsuit by a Northern California man who said he was shot during a party at Smith's house.
In the suit filed earlier this month in Santa Clara County Superior Court, David Kleczek, an attorney for Ronndale Esporlas, claims that Smith and former Niners tight end Delanie Walker fired weapons illegally during a party at Smith's San Jose home on June 29, 2012.
The players charged a $10 admission and $5 per drink, the lawsuit said. Smith, 23, and Walker, who is also named in the suit, were allegedly intoxicated on Smith's balcony when they later fired gunshots in the air while trying to end the party, the lawsuit said.
Kleczek said they then moved to the driveway where he alleged more shots were fired. Esporlas, 21, was shot twice in the leg while he was "caught in the crossfire between the two groups of people firing gunshots at each other," the lawsuit said.
As a result, Esporlas, "sustained serious, catastrophic and permanent injuries," the lawsuit said. The lawsuit seeks unspecified damages.
Attorneys for Smith and Walker, 29, have said Esporlas "freely and voluntarily exposed himself to all risks of harm" by attending the party.
They say injuries suffered by Esporlas, who was shot in the leg, were not caused by the defendants.
Santa Clara County prosecutors have said they are considering criminal charges.