Smith, 24, will be eligible to return to the 49ers' active roster on Nov. 10 following the team's Nov. 9 game against New Orleans.
According to ESPN.com, the suspension is broken down in two parts: four games for violations of the substance-abuse policy and five games for violations of the personal-conduct policy.
"Our organization has known this decision would come and we have prepared for it," 49ers general manager Trent Baalke said in a statement. "Aldon has taken responsibility for his actions and has continued to show growth personally and professionally. We will continue to support him, but it is time to put this matter behind us and focus on the season ahead."
Smith will lose $1.24 million of his $2.34 million salary, ESPN.com reported.
Smith was sentenced in July to 11 days of work release in a Santa Clara County (Calif.) court after his September 2013 arrest for drunken driving. It was his second such arrest since entering the NFL in 2011.
Smith also had three felony gun charges knocked down to misdemeanors.
Smith voluntarily missed five games last season when he entered a substance-abuse treatment center.
In April, Smith was arrested on an alleged fake bomb threat, but the Los Angeles City Attorney's office declined to press charges.
Smith was the No. 7 overall draft pick in 2011. He has 42 sacks in 43 regular-season games.
Smith's suspension comes on the heels of two other high-profile suspensions.
In July, Baltimore Ravens running back Ray Rice was suspended two games after he allegedly struck his then-fiancee, and now wife, Janay Palmer unconscious during an altercation at an Atlantic City hotel.
Surveillance video surfaced online showing Rice dragging an unconscious Palmer out of an elevator.
On Wednesday, Cleveland Browns wide receiver Josh Gordon, who has failed multiple drug tests, had his one-year suspension upheld by the NFL. Gordon's punishment was based on guidelines established between the league and the players' union in the collective bargaining agreement in 2011.
On Thursday, commissioner Roger Goodell announced a dramatic new domestic violence policy for the league, admitting "I didn't get it right" with Rice.
A first offense under the new domestic violence policy calls for a six-game suspension, while a second offense would result in a lifetime ban.
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