The Broncs (9-9, 4-2) have won three in a row since losing 71-65 on the road to the Greyhounds (12-6, 4-2) on Jan. 4.
Stewart and Thompson had four points apiece in the final 1:13 after Loyola rallied from a 53-42 deficit to climb back to within two points, 54-52. The two players each had 15 second-half points.
Robert Olson scored 14 of his 25 points for Loyola in the first half, which ended with the Greyhounds in front 31-27. Olson sank 6 of 13 shots in the half while the rest of the Greyhounds were 5 of 20.
The Broncs held Loyola's Erik Etherly, who had scored at least 20 points in three straight games, to nine points on 3-of-12 shooting.