The Broncos had erased a 48-41 deficit with 2:39 remaining on a 1-yard touchdown run by Knowshon Moreno, and Danny Trevathan then picked off Cowboys quarterback Tony Romo on the subsequent possession, returning it to the Dallas 24-yard line.
After Broncos signal-caller Peyton Manning took three snaps to run the clock down, Prater was true on the field goal try.
Manning completed 33-of-42 passes for 414 yards, four touchdowns and an interception, passing Dan Marino for the second-most career passing yards in in NFL history with 61,371.
He also scored a touchdown on the ground for the Broncos (5-0).
Julius Thomas made nine grabs for 122 yards and a pair of scores, while Eric Decker chipped in with five catches en route to 87 yards and a TD.
Romo finished with 506 passing yards and five touchdowns, completing 25-of-36 attempts with an interception. He became just the seventh quarterback ever to throw for at least 500 yards in a game and lose.
Terrance Williams made four catches for 151 yards with a score and Dez Bryant racked up 141 yards and two TDs on six grabs for the Cowboys (2-3).
Jason Witten hauled down seven passes for 121 yards with a scoring grab in the loss.
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