Terrance Timmons ran for 74 yards and a score on 11 carries for the Jaguars (6-4, 5-3 Sun Belt).
Texas State led 17-10 at the break but a 46-yard field goal by South Alabama's Aleem Sunanon and a Vaughn scoring pass to Danny Woodson tied it up, 17-17 in the third. Early in the fourth, Timmons ran it in from 8 yards to put the Jaguars up 24-17.
The Bobcats' Will Johnson kicked a 31-yard field goal with 4:21 remaining to close the gap, 24-20. But in the last drive of the game, the Jaguar defense stopped Texas State four yards shy of a touchdown as time expired.
Tyler Jones threw for 300 yards and a touchdown for the Bobcats (5-5, 3-3).