Stephen Calvert threw for 447 yards and three touchdowns, and Liberty shocked Baylor, 48-45, in the season opener for both teams on Saturday.
Liberty (1-0), in its last season in FCS before beginning a transition to FBS in 2018, was a 33-point underdog coming in.
Baylor (0-1), playing its first game under new coach Mark Rhule, trailed for much of the game, but went ahead 31-27 with 5:37 left in the third on a Chris Platt 75-yard TD pass from Anu Solomon.
The Flames regained the lead with 24 seconds left in the third on a 13-yard TD pass from Calvert to Antonio Gandy-Golden, and twice extended their lead to 10 points in the fourth quarter on Calvert touchdown throws.
Baylor got back to within a field goal on a John Lovett 34-yard touchdown run with five minutes to go, but after the Bears forced a Liberty punt, they were reduced to a last-play Hail Mary attempt that was intercepted by, of all people, Calvert.