Alabama A&M trailed 17-10 in the fourth following Brian McCain's 1-yard TD run for Southern (3-6, 2-5) with 8:02 to play. The Bulldogs sent the game into overtime when Mason found Montaurius Smith for a 7-yard TD pass with 30 seconds left.
Mason has 13 passing TDs and nine rushing TDs in his past seven games.
The win snapped a two-game losing streak for Alabama A&M, which remains in first place in the SWAC's East division.
Southern's Slyvester Nzekwe ran for 105 yards on 16 carries, and Joseph threw for 148 yards and two TDs on 16-of-32 passing.