The right-handed Fernandez was found to have a tear in the ulnar collateral ligament earlier in the week. Manager Mike Redmond announced Thursday that Fernandez would have the ligament transplant operation.
The usual recovery time for Tommy John surgery is 12-18 months.
Noted surgeon Neal ElAttrache will perform the surgery.
MLB recently formed a committee to look into pitching injuries.
"I'm almost afraid to pick up the paper because of the bad news,'' Selig said, according to ESPN.com. "I'm very worried over the fact that it's happening with so much regularity, over and over. We have some great young arms, and it's very sad.
"Let's see if we can find out some answers. Nobody has them, I'll tell you that -- including the doctors and trainers. Everybody you talk to has a different opinion.''
Since the start of spring training, pitchers who have been diagnosed with torn elbow ligaments requiring the surgery include:
Atlanta Braves right-handers Kris Medlen, Brandon Beachy and Cory Gearrin; Arizona Diamondbacks ace Patrick Corbin; Oakland Athletics starters Jarrod Parker and A.J. Griffin; Tampa Bay Rays All-Star Matt Moore; New York Yankees starter Ivan Nova; San Diego Padres starter Josh Johnson; New York Mets closer Bobby Parnell; Kansas City Royals setup man Luke Hochevar; Detroit Tigers reliever Bruce Rondon; Houston Astros reliever Jose Cisnero and top Pittsburgh Pirates prospect Jameson Taillon.