Thomas then benefited from a two-shot swing at the par-four 17th, where he sank a three-footer for birdie after Matsuyama had three-putted for bogey, and also birdied the last to close with a four-under 69 in the PGA Tour's opening event of the year.
The 23-year-old from Kentucky, whose previous two victories on the circuit had both come at the CIMB Classic in Malaysia, finished with a 22-under total of 270 in the elite 32-man, winners-only field.
Matsuyama, who had triumphed four times in his previous five starts worldwide, placed second after closing with a 70.
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(Reporting by Mark Lamport-Stokes in St. Augustine, Florida; Editing by Andrew Both)
