Stewart spent last season as defensive special assistant with the Philadelphia Eagles following his dismissal in Dallas after spending the previous two years as defensive coordinator there.
He replaces John Skladany, who was let go after Houston's 47-20 loss to Air Force in the Armed Forces Bowl. The Cougars went 10-4 last season behind the No. 1 offense in the country. But they ranked 111th in the nation in total defense.
Stewart spent three seasons as a secondary coach in San Diego and began his NFL coaching career as a defensive backs coach with the Houston Texans from 2002-03.