Funk shot a 3-under-par 69 for a total of 19-under 269 at the Crosswater Golf Club.
The victory was Funk's fourth on the senior tour and second this year. He also won the MasterCard Championship in Hawaii, the opening event on the 2008 schedule.
"It feels good to come in with a major win," Funk said.
Mike Goodes closed with a 68 and finished second at 16-under 272.
Funk collected $392,000.
Goodes won $231,000, the biggest check of his career. He had four birdies on the final nine holes.
"I made the turn and saw what Fred was doing and knew I needed to have a good back nine to finish as high as possible," Goodes said.
Swim Week Miami Beach 2014 [PHOTOS]