Niese winced as he finished making a pitch to Tyler Pastornicky with one out and motioned to the New York dugout that he was hurt.
David Aardsma replaced him with the Mets trailing 3-2.
Niese allowed eight hits and three runs in 3 1-3 innings. The left-hander struck out five.
Niese missed a turn in the rotation with shoulder tendinitis, but avoided the disabled list. He received 12 days of rest before making his next start June 9, a no-decision against Miami in which he allowed two earned runs in 6 2-3 innings.
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