After Auburn took a 20-13 lead in the third quarter on a 4-yard run by Kerryon Johnson, Milton threw a 12-yard touchdown pass to Otis Anderson to tie the game.
The Knights thought they deserved a higher ranking after winning the American Athletic Conference and leading the nation in scoring, and they made a strong statement by beating Auburn (10-4).
Auburn suffered its second straight loss at Mercedes-Benz Stadium, where it was beaten by Georgia in the Southeastern Conference championship game one month ago.
After the interception return by Burkett gave UCF a 34-20 lead, Auburn's Eli Stove had a 7-yard scoring run with about four minutes remaining.
Auburn insisted motivation would not be a problem after the crushing loss in the SEC championship game, but the Tigers had no answer when the Knights regained momentum.
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