The Yankees announced their plan for the speedy left fielder before Thursday's game against the Oakland Athletics. The surgery will be performed next week by Dr. Christopher Ahmad.
Gardner has not played since April 17, when he suffered what was described as a bone bruise after attempting a diving catch against the Minnesota Twins. After experiencing multiple setbacks in his rehab. Gardner underwent an MRI exam this week.
Yankees manager Joe Girardi already had acknowledged that he was preparing to finish the season without Gardner prior to Thursday's announcement.
"It's unfortunate," Girardi said. "We missed some of the things he brings to our club."
Girardi said he's comfortable finishing the season with the Yankees' left-field combination of Raul Ibanez and Andruw Jones. Ibanez, who plays against right-handers, has 12 homers and 40 RBIs; Jones has 12 homers and 26 RBIs.
"They've done a great job," Girardi said. "Look at the numbers Andruw and Raul have amassed with homers and RBI, and we can use (Dewayne Wise) for defense late if you want to. They've done a good job.
"We do miss that speed element that Brett brought to the game, but I've been pleased with what these guys have."
Jeff Fletcher is a contributor to ESPNNewYork.com.