Team physician Dr. Christopher Ahmad performed the procedure in New York, which will likely end Gardner's season.
"Everything went well," Yankees manager Joe Girardi said. "We'll get a chance to see him when we get back [to New York] and get a better idea what we're looking at."
Gardner was limited to just nine games this season, injuring his elbow while making a diving catch against the Twins on April 17 at Yankee Stadium.
The 28-year-old suffered three setbacks on Minor League rehabilitation assignments before having the surgery. Gardner is expected to be ready for Spring Training next season.