The team said after the procedure Tuesday that he was expected to return to normal offseason training in 6-8 weeks.
The 6-foot Lowry missed 19 games this season, mostly because of a bacterial infection. He sat out Houston's final two games with the sports hernia.
Goran Dragic took over the starting job from Lowry in March and averaged 18 points and 8.4 assists in 28 starts. Lowry averaged 14 points and 6.6 assists in 47 games for the Rockets this season.