Derrick Gordon had seven points, six rebounds and a crucial block for the seventh-seeded Hilltoppers (14-18), who advanced to play No. 5 seed North Texas in the title game on Tuesday.
Western Kentucky led 65-63 when Brian Stafford missed a 3-point attempt for No. 3 seed Denver (22-9), and Royce O'Neale rebounded and tried a put-back attempt with three seconds remaining. Gordon swatted the shot, and McDonald got the rebound and made two game-sealing free throws.
The Hilltoppers shot 55.9 percent (19 of 34) from the floor and made 24 free throws (in 34 attempts) to the Pioneers' 12 (16 attempts).
Denver dropped to 0-8 when allowing at least 65 points.