The game-winning play came after Scott had rallied the Wildcats (8-5) from a 48-35 deficit with 1:48 left in the game.
He cut the deficit to 48-42 on a 2-yard pass to Austin Hill with under a minute to go and then added the decisive score after Arizona recovered a fumble on an onside kick with just 42 seconds remaining.
Scott hooked up with Garic Wharton and Hill on passing plays to put the ball at the Nevada 2-yard line with 22 seconds to play, then found Miller on a slant route in the end zone, with John Bonano's extra point icing the win.
Scott completed 28-of-46 passes for 374 yards, three touchdowns and two interceptions and also rushed for a score in the victory.
Cody Fajardo went 22-of-31 through the air for 256 yards, three TDs and two pick-offs while also running for 140 yards with a score for Nevada (7-6).