San Diego general manager Jed Hoyer said Tuesday that Gonzalez, who went to three different doctors for opinions on his shoulder last week, will have a procedure to "clean up" his right labrum in New York, Hoyer said.
Gonzalez is expected to be ready for the start of Spring Training in February.
"There's a sense of relief for him to get it done," Hoyer said.
Gonzalez first injured the shoulder diving for a foul ball in Houston in May. He guarded the shoulder to some extent the remainder of the season, not diving for as many balls as he might have otherwise.
Offensively, the shoulder changed the way Gonzalez hit. Instead of trying to pull the ball, he concentrated on hitting more line drives up the middle and to left field.
Gonzalez also switched to a lighter bat to alleviate the strain on his shoulder.
Consequently, Gonzalez had his best success against left-handed pitchers (.337 batting average and .424 on-base percentage) of his career.
Gonzalez, who recently completed his fifth season with the Padres, hit .298 with 31 home runs and 101 RBIs in 160 games. This marked the fourth consecutive season that he hit 30 or more home runs.
The Padres hold a $6.2 million option on Gonzalez ($5.5 million plus incentives that he has reached) for 2011 that they plan to pick up.