Alvin Leon Roundtree was arrested and charged with domestic violence Tuesday and remains in federal custody.
A joint FBI and San Antonio Police complaint said Roundtree approached the woman on the campus of the Army Medical Center and School at Fort Sam Houston after an argument over their recent separation.
He then allegedly pulled out his .45 caliber pistol and shot her several times.
"It started out as a conversation," said Col. Randy Anderson, commander of the center and school. "He came into her office space, and then she took him outside of the building."
Authorities caught up with Roundtree elsewhere on the Fort Sam grounds that afternoon. He faces up to 20 years in prison and a $250,000 fine.
The identity of the woman, who is active-duty Army and teaches at the school, has not been released, but she is in stable condition at San Antonio Medical Center.