Kirk finished at 22-under 266, carding six birdies and two bogeys to become the fifth rookie to win on the tour this season, joining Jhonattan Vegas, Charl Schwartzel, Brendan Steele and Keegan Bradley.
It was his third win as a professional -- Kirk had took a pair of Nationwide Tour victories last year.
He edged both Pernice (67) and McNeill (68) by a single stroke.
Pernice just missed his first PGA Tour win since 2001 while McNeill's four birdies weren't quite enough for the victory.
Sharing fourth place were Bud Cauley (67), Hunter Haas (68) and Jim Renner (68) at 20-under 268.
Swim Week Miami Beach 2014 [PHOTOS]