Harrison made only two starts last year and was making only his fourth of this season after undergoing two surgeries on a herniated disc in his lower back. He allowed three runs on four hits and three walks on Tuesday and was tagged with the loss.
The 28-year-old, who is 6-foot-4 and 240 pounds, was an All-Star in 2012, when he went 18-11 with a 3.29 ERA in 32 starts.
There was no word on the severity of the injury, according to T.R. Sullivan of MLB.com. The temperature in Houston was a cool 66 degrees at the start of the game, Sullivan reports, and the roof was open at Minute Maid Park.
Harrison is 1-1 with a 4.15 ERA in four starts this season with 10 strikeouts and 12 walks in 17 1/3 innings. SI WIRE: Marlins pitcher Jose Fernandez will seek second opinion on Tommy John surgery