The move came after Lyles gave up three runs, five hits and four walks over three innings in a 5-3 loss at Milwaukee on Saturday.
Pirates manager Clint Hurdle said Lyles' hamstring problem caused "collateral damage" to the bullpen. Hurdle said he thought the injury affected Lyles' delivery.
Lyles is 5-3 with a 3.64 ERA in 12 starts.
Right-hander Montana DuRapau was recalled from Triple-A Indianapolis before Monday night's game against the Atlanta Braves.