The veteran Victorian - wearing a sponsor-less hat and shirt - had slept on a one-shot 54-hole lead and his opening birdie preserved his advantage over the field at Coco Beach Golf Club in Rio Grande.
But there was no fairytale result for Baddeley, whose challenge slowly evaporated over the course of the afternoon.
Three bogeys in four holes from starting at the 5th suggested the 37-year-old’s chances of recording his first win anywhere since the 2016 Barbasol Championship were slim.
Consecutive pars from the 9th to the 14th effectively ended Baddeley’s run as little-known American Martin Trainer, playing in the group ahead, emerged as the likely champion.
Once Trainer reached the 72nd hole – a reachable par-5 – he was two shots clear of the field and three clear of Baddeley and his eventual closing birdie sealed his first PGA Tour win with a 15 under total.
Baddeley followed with a closing birdie of his own to jump into a four-way tie for second at 12 under with Americans Johnson Wagner and Daniel Berger and Canadian Roger Sloan.
Despite the heartache of letting a golden opportunity slip, Baddeley’s high finish not only nets him a hefty windfall but is projected to lift him 33 places higher in the FedEx Cup standings to 54th.
Cameron Davis was the next best Australian in Puerto Rico, sharing 16th, followed by Curtis Luck (T25).
Robert Allenby and Stuart Appleby shared 49th, Matt Jones was 55th and John Senden 62nd.
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