Eckroat edged out fellow Americans Justin Lower and Carson Young, who both carded 65s and tied for second, one shot ahead of Max Greyserman (65).
Playing in the group ahead of Lower and Young, Eckroat birdied the par-4 17th to open a three-stroke lead over Young, then finished with a bogey on the par-5 18th at Tiger Woods-designed El Cardonal at Diamante.
He finished at 24-under 264. The 25-year-old former Oklahoma State player won the Cognizant Classic in March at PGA National for his first PGA Tour title.
Eckroat locked up spot in the top 50 in the FedExCup Fall standings with Sunday's win.
"I think it kind of validates the season that I had, just a great way to cap off and end the year," Eckroat said. "It was really special to do it at an event where the title sponsor, I'm an ambassador of their company. A cool week."
Needing an eagle to force a playoff, Young birdied the 18th.
"I hit a bunch of good iron shots, especially on the back nine," Young said. "I shot 7 under, so I played good, I can't be too mad about it."
Lower closed with an eagle for his 65.
"I played well," Lower said. "I said yesterday I had to shoot probably somewhere between 5 and 9 again just to have a chance. Shot 7 and came up one short."
On Sunday, Eckroat didn't have a par until the seventh hole, opening with five birdies and a bogey. He added a birdie on No. 8 and birdied four of the first five holes on the back nine.
"That's probably some of the best golf I've ever played, just from the start putts were going in," Eckroat said.
"I don't know, it was automatic out there today, I guess, is how you could call it. It's crazy I only won by one shooting 9-under par today from one back. Obviously, everybody was playing well, it was a good battle."
Lone Australian Aaron Baddeley was well back, tied 64th at three under after a 75.
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