Marte was not available for comment after the game. Manager Clint Hurdle described the condition as "recurring."
"It originally happened [on Tuesday] night; he felt a twinge," Hurdle said. "It's a weird kind of thing. It doesn't show up all the time, but it showed up tonight, repeatedly."
Marte did not take the field at the start of the third, two innings after aggravating the discomfort while fouling off a pitch from Cardinals right-hander Michael Wacha. Sean Rodriguez replaced Marte in left.
Marte indicated discomfort in the hand after hitting an opposite-field foul in the top of the first. Assistant trainer Ben Potenziano checked him out, with Hurdle looking on, then Marte finished the at-bat, fouling out to first base.
He remained in the game and made the last out in the top of the third, again hitting an opposite-field popup.
"We'll have him re-examined [on Thursday]," Hurdle said.
General manager Neal Huntington was made aware of Marte's status and will pay close attention to the diagnosis to see whether a roster move will have to be made.