Shorts played through a groin injury for much of the season, then re-aggravated it two weeks ago. He was held out of the Jags' loss to the Buffalo Bills last Sunday.
While Shorts initially said the procedure could wait until the offseason, the team opted not to rush the 25-year-old back in the midst of a 4-10 rebuilding year.
Shorts has paired with Justin Blackmon, who was suspended for the remainder of the season in November for violating the league's substance abuse policy, to become one of the best up-and-coming receiving tandems in the NFL. A fourth-round pick in the 2011 draft, Shorts finished 2013 with 66 receptions for 777 yards and three touchdowns.
Oehser also noted that guard Mike Brewster had ankle surgery on Wednesday.