The surgery was performed by Dr. James Andrews.
Brees will return to San Diego next week and begin rehabilitation. He is expected to begin throwing in four months and be ready to participate in training camp.
"Though his recovery period is longer than we had hoped for, we couldn't be happier that Drew is expected to make a full recovery," general manager A.J. Smith said in a statement.
The Chargers must decide by Feb. 23 whether to designate Brees as their franchise player again and give him a one-year deal worth about $10 million. Brees, who has wanted a long-term deal, played the 2005 season under an $8 million contract as the franchise player.