The reigning National League Cy Young Award winner had cruised through the start, fanning four over four scoreless innings before eventually feeling the tightness. Alcantara is now traveling back to Miami to be evaluated by the team.
Alcantara has been sidelined since Sept. 6 because of a right forearm flexor strain. He first felt discomfort while pitching against Washington on Sept. 3.
The Marlins right-hander was working his way back in the hopes of rejoining the team amid a tight NL wild-card race. The Marlins entered Friday 0.5 games back of the Chicago Cubs for the final spot.
Before going on the injured list with the first arm-related issue of his big league career, Alcantara had thrown 184⅔ innings and three complete games, going 7-12 with a 4.14 ERA and 151 strikeouts.
The Associated Press contributed to this report.