Haas, who started the round with a four-shot lead, offset five bogeys with five birdies to finish with an even-par 72 and 15-under-par total 273, three clear of his playing partner and nearest rival Michael Allen.
Compatriot Allen finished second after shooting a 71 while fellow American D.J. Trahan and Zimbabwe's Brendon de Jonge tied for third a further stroke back at 11-under.
"I always said, after winning one, you want to win two. Now I want to win a third," Haas said.
His victory in the first of four Fall Series tournaments lifted him to 26th on the money list. The top 30 at the end of the season receive an automatic place in next year's U.S. Masters and U.S. Open.
Haas was joint leader after the first and second rounds and never trailed in the tournament but made a bad start to his final round, dropping a shot at the first hole.
He had another four bogeys on the back nine and briefly dropped back into a tie with Allen, but made up for his blemishes with five birdies.
"I had to handle my nerves since the first hole but it's just not easy," said Haas. "I remember feeling it at the Bob Hope. I didn't feel any different today. I felt nervous."
He has never won on the PGA Tour in 357 tournament appearances and this was the third time he finished second.
He drew level with Haas after the 12th hole but his chances evaporated when he made a double bogey on the next hole when he got an unlucky bounce with a drive that found the fairway.
"It looked like he was starting to get a little nervous or play a few straight shots, and I was kind of gaining on him," Allen said.
"I really hit a good drive on 13 but it was just a terrible bounce. Ball bounced 30 yards left and out of bounds."
(Reporting by Julian Linden in New York; Editing by Frank Pingue)