Trailing 35-31 with under 2 minutes to go, Herb Walker Jr. caught the 17 yard game-winner to put Morgan State up by three and then Hampton's final drive stalled at its own 37, with the Pirates turning it over on downs.
Skillon added 45 yards rushing on 12 carries and another touchdown for Morgan State (5-4, 4-1 Mid-Eastern Athletic), while Walker finished with seven catches for 109 yards and added 67 more yards on the ground, including three touchdown runs.
Five touchdowns were scored in the final quarter and the lead changed five times.
Jerell Antoine passed for 164 yards and two touchdowns for Hampton (2-7, 1-4), despite throwing two interceptions. Mixon caught six passes for 83 yards and a touchdown.