The Spurs said Aldridge underwent an arthroscopic subacromial decompression and rotator cuff debridement on his right shoulder. Dr. Daniel Cooper performed the procedure April 24 in Dallas.
"Disappointed I won't get to finish the season with my teammates, but excited that I'll be fully ready to go next season and beyond," Aldridge said in a statement.
Aldridge, 34, initially injured his shoulder during a game against the Utah Jazz on Feb. 21. He played in San Antonio's next matchup but went on to miss the next six contests.
The veteran forward returned in the Spurs' victory against the Dallas Mavericks the day before the NBA suspended its season because of the coronavirus pandemic.
NBA owners and the NBA Players Association recently agreed to resume the 2019-20 season in Orlando, Fla., under a 22-team format. The Spurs are one of those 22 teams set to return to competition near the end of July.
The loss of Aldridge, a seven-time All-Star selection, will be a big blow to the Spurs as they continue their quest for a 23rd consecutive playoff berth. He averaged 18.9 points and 7.4 rebounds in 33.1 minutes per game this season.
The Spurs expect Aldridge to be fully cleared for all basketball activities before training camp begins for the 2020-21 campaign.