Assistant athletic trainer Ben Potenziano ran out from the dugout to check on Marte, who walked off the field with Potenziano and manager Clint Hurdle shortly afterward.
"I just felt it was best to get him out at that particular time of the game," Hurdle said. "Where we stood [trailing, 10-1], there was no need for him to continue to try to play through."
Marte has been arguably the Pirates' best all-around player this season, batting a team-high .331 with 20 stolen bases while maintaining his Gold Glove-caliber defense in left field. Marte was moved from left to center field after six innings because the Pirates subbed Andrew McCutchen out of the game.
McCutchen, who went 0-for-3 with three strikeouts, was not removed due to injury concerns.
"He was taken out just because he'd been run down," Hurdle said. "There was no injury there."
With their position-player options exhausted after Marte's exit, the Pirates moved first baseman John Jaso to right field, sent Matt Joyce from right to left and shifted Gregory Polanco from left to center. Catcher Erik Kratz entered the game to play first base, though he later pitched the ninth inning, with catcher Chris Stewart, who pinch-hit in the eighth, remaining in the game at first.
Marte returned to the Pirates lineup Sunday night, his first start since he was struck in the face by a one-hopper in left field Wednesday.
Two weeks ago, he exited the first half of the Pirates' doubleheader against the Mets with a bruised left ankle but played the following day, June 8, and returned to the starting lineup June 9.
Adam Berry has covered the Pirates for MLB.com since 2015. Follow him on Twitter at @adamdberry. This story was not subject to the approval of Major League Baseball or its clubs.