Gomber, acquired by Colorado in the offseason as part of the trade that sent star third baseman Nolan Arenado to St. Louis, was placed on the 60-day injured list with a condition know as pars defect. It refers to stress fractures of small bones in the lower spine, typically caused by overuse.
The 27-year-old Gomber is expected to recover with rest.
"It's going to keep him out for the rest of the season," manager Bud Black said. "He'll be fine in a month or two. It won't impact his offseason. It won't impact next season."
Gomber, who was 9-9 with a 4.53 ERA, had been dealing with back pain for the last couple of weeks, Black said.
Gomber didn't make it through the fifth inning in either of his last two starts, both losses. Team doctors conducted further tests and discovered the stress reaction condition.
Black said Gomber's scheduled start Sunday against Atlanta will now be made by right-hander Ryan Feltner, who was called up from Double-A Hartford. Feltner will be making his major league debut.
In other moves, the Rockies placed infielder/outfielder Connor Joe on the 10-day injured list with a strained right hamstring. Joe was hurt while running the bases during Friday night's game against the Braves.