Dr. Robert Watkins repaired a herniated disc in Pierre-Paul's lower back at a hospital in Marina Del Rey, Calif. It's expected it will take about three months for the player to fully recover.
Pierre-Paul, 24, played with the back injury last year and received epidural injections to get through the season.
Ronnie Barnes, the Giants senior vice president of medical services, said having the operations was "the most prudent course of action."
"We expect a full and complete recovery," Barnes said.
Pierre-Paul acknowledged he played through the pain last season.
"The treatment I've been doing has helped manage the issue, but this procedure is going to get me fully healthy and there should be no more pain," he said. "I'm going to do everything the doctors tell me to do during my rehab so I can be back playing the game I love at a high level as quickly as possible."
The Pro Bowl pass-rusher's sack statistics declined from 16.5 sacks in 2011 to 6.5 in 2012.