Wang allowed four runs and six hits before he was replaced in the sixth inning. Wang, who missed time earlier this season with weakness in the adductor muscles in his hips, went for an MRI that revealed the shoulder strain and bursitis.
"It was unfortunate because I thought today was his best start," said manager Joe Girardi, who wasn't sure yet what the Yankees would do about Wang's next turn in the rotation. "He'll need some rest."
Wang surrendered a two-run homer to Adam Lind with one out and threw a pitch to Scott Rolen before catcher Jorge Posada motioned to the dugout that something was wrong with the right-hander. Girardi and assistant trainer Steve Donohue came out to the mound, and Wang headed for the dugout after a short discussion.
"Just the way he threw the ball," Posada said. "It wasn't like he followed through all the way through, kind of pushed it towards me."
Wang also had shoulder problems in 2001 and 2005 but he said it was less painful this time and only bothered him on the pitch to Rolen.
"On the home run pitch it felt a little tight but not pain," he said.
The Yankees could turn to Phil Hughes or Alfredo Aceves if Wang can't make his next start, but neither is stretched out enough to go deep into a game. Hughes worked a perfect eighth as New York beat Toronto 6-5 in 12 innings Saturday.
Wang was awful at the beginning of the season but had looked better of late, earning his first win of the season in his previous outing and pitching at least five innings in each of his last four starts.
Wang, who won 38 games from 2006-07, is 1-6 with a 9.64 ERA in 12 games, nine starts, this season.