The 23-year-old Kaprielian is rated as the Yankees' No. 6 prospect and the No. 55 overall prospect in baseball. Recovery time for Tommy John surgery is generally estimated to be between 14 and 16 months.
"It's definitely not what we wanted," Yankees manager Joe Girardi said. "Our hope was that he could pitch this whole year and really make some strides toward being a pitcher for us, but that's not going to happen."
The No. 16 overall selection in the 2015 Draft, Kaprielian has made just 14 professional appearances due to continuing flare-ups in his right elbow. He missed all but three games last season before showing promise in seven Arizona Fall League appearances, over which he posted a 4.33 ERA.
After a clean spring, Kaprielian was scratched from his first start for Class A Advanced Tampa after reporting a recurrence of pain in his elbow. He had an MRI and a dye contrast MRI performed in Tampa, Fla., after which the Yankees recommended surgery.
"I feel for the kid. He worked very hard to get back," Girardi said. "He worked, he went to the Fall League, he worked very hard to get ready for Spring Training. It wasn't meant to be. My heart goes out to him because you see the look in his eyes every time that he takes the mound. You understand how bad this kid wants to be here and pitch in the big leagues."
Yankees general manager Brian Cashman said on Wednesday that ElAttrache agreed with the team's recommendation.
"You see the ability that he possesses, but you have to be healthy to be able to harness it," Cashman said. "You know it's there and at some point we're looking forward to having it for an extended period of time.
"Injuries are also part of the game and you have to deal with them. Unfortunately right now, the front of his pro career has had some injuries with that elbow, but he has an opportunity to have a very long career regardless."
Bryan Hoch has covered the Yankees for MLB.com since 2007. Follow him on Twitter @bryanhoch and on Facebook. This story was not subject to the approval of Major League Baseball or its clubs.