Wagner, whose only other PGA win was at the 2008 Houston Open, finished 54 holes at 13-under-par 200.
He bypassed second-round leader Chris Stroud, who tumbled into second place with a 1-under 70 and finished the day at minus-12 at El Camaleon Golf Course in Playa del Carmen, Mexico.
Knotted for third one shot further back at minus-11 were Bobby Gates (64), Spencer Levin (67) and Jarrod Lyle (67).
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