Brisly Estime set up Hunt's touchdown with a 70-yard punt return.
Syracuse (7-6) led 14-3 entering the fourth quarter before Mitch Leidner threw two touchdown passes and a 2-point conversion to put the Golden Gophers up 17-14.
After the Orange regained the lead, Minnesota attempted two long passes to the end zone on the final plays. The first slipped through the arms of Drew Wolitarsky and the final Hail Mary as time expired was knocked down near the end zone.
Minnesota (8-5) got a boost to start the second half when coach Jerry Kill returned to the sideline for the first time since Sept. 28 before Syracuse rallied for the victory.
Hunt finished with 188 yards passing and 74 rushing with two scores.
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