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.
ESPN's Dan Dakich joins The Paul Finebaum Show to discuss the SEC's presence in the NBA Draft.
Ted Kapita was the top-rated recruit from West Virginia in the class of 2015 and recently played at DME Academy in Florida.
With the Suns drafting Tyler Ulis, they now have five guards on their roster who attended Kentucky.