Scott began the final round two shots behind the leaders, David Toms and Hideki Matsuyama, and with four birdies in his first six holes appeared to be on track for victory before a double bogey at the 9th hole, where he found the trees from the tee and then three putted, threatened to cost him not only a victory but possibly his newly earned world number one title.
With Henrik Stenson having finished tied for 7th in England a few hours earlier Scott needed a top 13 to retain his standing atop the world ranking and he responded to the near disaster gamely with three birdies in the opening five holes of the back nine and eventually recorded a round of 66.
He had a share of the lead with Dufner who had also recorded a final round of 66 and although the pair were forced to wait nearly an hour until the final pairing had finished, their 72 hole totals stood up.
Both halved the first two extra holes in pars and then birdies before Scott hit a superb tee shot and an approach to 7 feet and the 3rd and claimed the title.
Nicholas Thompson and Freddie Jacobsen finished in a tie for third.
In winning Scott became the first man to have all four titles in Texas to his name and also completed a great season in Texas for the Australians generally with Steve Bowditch and Matt Jones winning in San Antonio and Houston respectively.
Scott will draw more than one point clear of Stenson who takes over as the world number two from Tiger Woods.
For the record Scott earned US$1,152,000.
John Senden continued his very good season when he finished in a share of 5th position, his third top five of the season and added another US$216,000 to his coffers.
Marc Leishman shared 21st position with eight others, a bogey at the last potentially costing him an automatic spot in the US Open. That won't be confirmed until the revised rankings are finalised in the next few hours but had he parred the last then he would have been assured of being inside the top 60 by today and guaranteed of exemption into the US Open at Pinehurst.
He still has another opportunity next week and in Sectional Qualifying if he does not make it today which now appears unlikely.
The PGA Tour now heads to Dublin in Ohio for the Memorial Tournament at Muirfield Village.