Joyce struck out in the seventh, and Sean Rodriguez entered the game to play left field in a double switch before the eighth inning.
Marte is batting .321/.365/.482 with five home runs, 21 RBIs and 18 steals this season. He is being evaluated by the Pirates' training staff, the club announced. There was no further indication regarding the severity (or lack thereof) of his injury.
Between the first and second games of Tuesday's doubleheader, Pirates manager Clint Hurdle said Marte was dealing with a bruised ankle that "complicated" his mobility in the outfield.
Marte was not in the Pirates' Game 2 lineup. Joyce started in right field, and Gregory Polanco moved over to left.
The Pirates had just returned to full strength on Tuesday, as infielder David Freese and catcher Francisco Cervelli were in the Game 1 starting lineup after sitting out all weekend due to injuries.
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.