Kisner began the day with a two-stroke lead and finished at 13-under 275 after a tumultuous final round in the tournament featuring 80 professionals from the PGA, LPGA, Champions and Web.com tours.
"I wish I would had about a six-stroke lead, so it wasn't so stressful," said Kisner, who rejoined the PGA Tour this season. "The back nine was playing brutally hard. I just got unlucky."
Kisner, who had a tournament-low 64 Saturday at Spyglass Hill, moved to 17 under and a six-stroke margin after 11 holes. But he bogeyed the 12th, double-bogeyed the 14th and bogeyed the 17th.
"I just hung in there," said Kisner, who in March claimed his second Web.com Tour win at the Chile Open in Santiago. "Things like this always happen when you are in the hunt. Only when you are in a position to win does it seem to happen."
Hadley, playing in the final group with Kisner, began the day trailing by five shots. But he remained steady while Kisner stumbled.
"When Kevin double-bogeyed 14, I definitely thought I still had a chance," said Hadley, a 2014 PGA Tour rookie. "The conditions were tough out there, but I thought I had a chance on the 18th, but Kevin made a downhill 15-footer to win. My hat's off to him."
Brooks, who has won the event three times, moved into contention and was six under on the day and 11 under for the tournament halfway through the final round before faltering.
Jason Kokrak started the day in second two shots back, but shot 80 and finished among seven players at 283.
Hall of Famer Annika Sorenstam, who has played in the event several times since retiring from the LPGA in 2008, finished at even par after a final-round 75.
Kisner earned $60,000 of the $300,000 purse.