The All-Pro's suspension broke down into four games for violations of the substance abuse policy and five games for violations of the personal conduct policy, a league source told ESPN's Ed Werder. Smith will be allowed to be in the team's facility for meetings while under suspension, according to ESPN sources and multiple reports.
"I apologize to my teammates, coaches, the entire 49ers organization and 49ers fans for not being able to contribute on the field for the next several weeks," Smith said in a statement released Saturday by the NFL Players Association. "Over the last year, I have learned a lot and I'm working hard to grow from my experiences. I want to thank my family and friends, my teammates, my union and the 49ers for supporting me during this process. I will be at work daily to participate in all permitted work activities, and to support my teammates, just as they have supported me."
Smith will be eligible to return to the 49ers' active roster Nov. 10 following the team's Nov. 9 game against New Orleans.
"Our organization has known this decision would come, and we have prepared for it as a team," 49ers general manager Trent Baalke said in a statement Friday. "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."
Based on the length of the suspension, Smith will lose $1.24 million of his $2.34 million salary, ESPN business analyst Andrew Brandt reports.
Smith, who met with commissioner Roger Goodell the first week of August, 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. Also, Smith 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 October, in London, Goodell told reporters Smith's aggressive approach to his problem could be considered when potential discipline was addressed. However, it did not ultimately impact his punishment, a source told Werder.
Smith was suspended two days after Browns wide receiver Josh Gordon's indefinite suspension by the NFL was upheld. Gordon will miss at least 16 games for another violation of the league's substance abuse policy.
Smith has repeatedly said he has been sober since his DUI arrest last September. He played in a 27-7 home loss to the Colts on Sept. 22, two days after he was arrested and jailed on suspicion of DUI and marijuana possession. After the game, he publicly apologized for his behavior and later announced he would leave for treatment.
While the Niners went on a five-game winning streak without him, Smith's menacing presence was sorely missed. The team still picked up his 2015 contract option this spring.
The 49ers, who went 14-5 last year and lost to the Super Bowl champion Seattle Seahawks in the NFC Championship Game, also are without injured All-Pro linebacker NaVorro Bowman for at least half the season as he recovers from a left knee injury that required surgery after the NFC title game.
Coach Jim Harbaugh and defensive coordinator Vic Fangio have expressed their confidence in the linebackers, who will be called upon to fill in with Bowman and Smith out -- including rookie Chris Borland, Dan Skuta, Michael Wilhoite and Corey Lemonier.
Third-round draft pick Borland made his case for a starting spot with a 34-yard interception return for a touchdown in Thursday night's 40-13 preseason win at Houston.
In his latest run-in with the law, Smith was arrested April 13 at Los Angeles International Airport. Police said Smith was randomly selected for a secondary screening and became uncooperative with the process, telling a TSA agent that he had a bomb. No charges were filed.
In November, he pleaded not guilty to three felony counts of illegal possession of an assault weapon, stemming from a June 2012 party at his home. Investigators said several shots were fired, two partygoers were injured and Smith was stabbed. In the subsequent investigation, prosecutors say detectives found five unregistered, illegal weapons in Smith's house.
Last season, Smith finished with 8½ sacks and 34 tackles in 11 games with eight starts. He was initially worked back in slowly, but demonstrated he had stayed in shape while away.
Selected seventh overall in the 2011 draft out of Missouri, Smith had a franchise-record 19½ sacks during the 2012 season for the 49ers, who lost to Baltimore in the Super Bowl after that season.
Information from ESPN.com Raiders reporter Bill Williamson and The Associated Press was included in this report.