Peterson caught a 38-yard touchdown pass from Driphus Jackson in the second quarter and capped the scoring with an 8-yard TD run with 3:37 left in the game for the Owls (3-6, 1-4 Conference USA).
Jackson completed 4 of 6 passes for 92 yards and two touchdowns in relief of starter Taylor McHargue, who took a hit on his injured shoulder in the second quarter and did not return.
Southern Miss (0-8, 0-4) turned the ball over five times and remained winless this season despite gaining more yards -- 372 to 370 -- than the Owls. Tracy Lampley had four receptions for 101 yards for the Golden Eagles.
One of Southern Miss' turnovers was a 75-yard interception return by Rice's Paul Porras that gave the Owls a 31-10 lead in the third quarter.