Redshirt senior quarterback Cole Weeks went 20/46 for 309 yards and a touchdown with two interceptions and a fumble.
The Golden Eagles were down 21-14 entering the 4th quarter, but a Weeks interception off a deflected pass was returned 51 yards for a touchdown by UTEP's Trey Brown with 13:12 left in the game.
Later in the quarter after a sack caused a forced fumble, Miners defensive player Nick Gathrite returned the ball 59 yards for a touchdown to give UTEP a three score lead with 9:31 left to play.
Southern Miss' defense only allowed 234 total yards to UTEP.
The Golden Eagles tied the Miners at 7 in the 3rd, when Weeks completed a 55 yard touchdown pass to Casey Martin with 11:54 remaining in the 3rd quarter, but the special team's unit gave up a 98 yard kickoff return on the next possession to make it a 14-7 game.
USM's Rakeem Nunez-Roches blocked a 34-yard field goal attempt and Cornell Armstrong returned it for a touchdown with 1:54 left in the 3rd quarter to make it a 21-14 contest.
UTEP forced five turnovers total (two interceptions, three fumbles).
Southern Miss returns to Hattiesburg to face the Marshall Thundering Herd (8-0), November 8. Kickoff is set for 6 p.m.