The recovery time for Tommy John surgery is approximately 12 to 18 months.
"We had an inkling that was going to be the recommendation," manager Joe Girardi said. "It's unfortunate, and obviously he has to make a decision now. It's what you don't want to hear."
Girardi said that he had not spoken to Nova, who sustained the injury during Saturday's start against the Rays at Tropicana Field, but the Yankees have already decided how they will patch the hole left by Nova's departure.
Vidal Nuno, who pitched five scoreless innings in a spot start against the Rays on Sunday, will slide in as the fifth starter for the foreseeable future. Nuno's next start has been set for Saturday against the Angels at Yankee Stadium; Nuno has a 6.75 ERA in four games (one start) this year.
"He pitched extremely well," Girardi said. "Now you would think that you could move him to 80, 85 pitches the next time, which is almost where our starters were the first start; pretty close."
Girardi said that Nova has the option to seek another opinion before undergoing surgery. Nova was 2-2 with an 8.27 ERA in four starts for New York this season, including allowing a career-high four homers allowed in his last start.
"We had high hopes for him because of what he did at the end of last year," Girardi said. "His Spring Training was very, very good. We had big expectations for him. This is a blow to our rotation, but no one is going to feel sorry for you. As a ballclub, we have to figure it out."
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.