Humphries was 32 of 51 for 286 yards and Clay had 118 yards as Murray State (2-4, 1-2 Ohio Valley) ran up a 31-6 halftime lead.
Pokey Harris returned the opening kickoff 61 yards to set up the Racers' first drive, which ended on Humphries' 1-yard plunge. Austin Peay fumbled on its first possession, and Murray State moved it 43 yards in 11 plays, culminating in Clay's 2-yard score.
Austin Peay (0-6, 0-3) used a seven-play, 51-yard drive for Taye Davis' 6-yard touchdown run, but Murray State responded with 17 points in the second quarter, including Clay's 9-yard touchdown run and Humphries' 3-yard score.
The Governors added touchdown runs by Jared Beard (10 yards) and Kendall Morris (62 yards) in the second half.