The shop is in the West Memorial subdivision near the Katy Freeway, and not far from Highway 99.
The incident happened at about 2 a.m.
According to Harris County Sheriff Ed Gonzalez, one male was wounded and transported to the hospital and a second male fled and is still on the run.
Detectives are also questioning a female who Gonzalez calls a "possible suspect."
The owner of S&T Autobody saw the intruders breaking into his business on a video link.
He went to the shop and they were still there. He shot at them, striking at least one man.
Covering Katy will update this story as more information is made available.