The 24-year-old Smith entered his plea Wednesday in Santa Clara County Superior Court.
Prosecutors say Smith faces a range of possible sentences, from spending no time in custody to a maximum of four years and four months behind bars. Sentencing is set for July 25, 13 days before the 49ers' preseason opener against the Baltimore Ravens.
"We are aware that Aldon entered a plea today in a case that we have closely monitored," 49ers general manager Trent Baalke said in a statement. "Today was an important step towards bringing that situation to a resolution. Any further questions concerning today's hearing should be directed to his attorney."
In November, Smith pleaded not guilty to three felony counts of illegal possession of an assault weapon after deputies said they found three assault rifles while responding to a complaint about a party in June 2012 at Smith's home. Prosecutors say those rifles are illegal in California.
The DUI charges were filed after Smith's car collided with a tree in San Jose in September and police said his blood-alcohol level was twice the legal limit.
Information from The Associated Press was used in this report.