The pair needed a playoff to decide the winner after each finished 72 holes with a tournament-record 18-under-par 198. Allen carded a 3-under 69 and Waldorf fired a 5-under 67 in the final round to catch him atop the leaderboard.
Both golfers birdied the par-5 18th at Broken Sound Club on the first extra hole, forcing them to replay No. 18.
Allen put his tee shot into the right rough, then used a spectacular second to get within 30 feet of the pin. Waldorf, meanwhile, pulled his approach into a greenside bunker and blasted out to within 7 feet.
Allen 2-putted for birdie, but Waldorf's try missed, handing Allen the win.
Third place went to Chien Soon Lu (69) at minus-17.
Chipotle plans first price increase in 3 years
Putin thinks Obama would save him if he were drowning