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Beljan carded a three-under 69 final round, countering a double-bogey and three bogeys with eight birdies for a 16-under total of 272.
Matt Every and Robert Garrigus both shot four-under 68 in the final round to share second place on 14-under 274, and Brian Gay was a stroke further back after a 70 for 275.
Beljan, who came into the final tournament of the season at 139th on the money list, needed a good week to move into the top 125 and secure full playing privileges for next season.
With the victory he's guaranteed his tour card for the next two seasons and a berth in the PGA Championship, but for a time it looked as if he wouldn't even be able to finish the tournament.
Beljan was in hospital on Friday night, after an apparent panic attack had him battling shortness of breath, an elevated heart rate and light-headedness during the round.
He even told his caddie he thought his life was in jeopardy, but he opted to return to the course on Saturday and had emerged from the third round with a two-shot lead.
On Sunday he briefly fell into a tie for the lead, but a run of five birdies in a six-hole span starting at the seventh saw him pull away.
Despite a double-bogey six at the par-four 13th, he managed to hang on for the win.
Tim Herron closed with a 69 to finish tied for ninth, just squeaking into the top 125.
But there was disappointment for some who started the week on the edge.
Australian Rod Pampling and Billy Mayfair, who both missed the cut, fell to 127 and 128 respectively. Their status in the top 150 will give them partial status for next year, allowing them into some events but not all.
Leading final-round scores on Sunday in the $4.7 million US PGA Tour event at Disney World Resort (USA unless noted, par-72)272 - Charlie Beljan 68-64-71-69
274 - Matt Every 67-69-70-68, Robert Garrigus 68-68-70-68
275 - Brian Gay 69-69-67-70
276 - Scott Stallings 66-70-71-69, Josh Teater 71-67-67-71, Boo Weekley 70-67-72-67, Charlie Wi (KOR) 64-71-70-71
277 - Mark Anderson 68-67-74-68, Tom Gillis 72-66-70-69, Tim Herron 71-70-67-69, Jerry Kelly 71-68-72-66, Russell Knox (SCO) 66-72-72-67, Joey Snyder 69-70-72-66
278 - Cameron Beckman 70-68-69-71, Charles Howell 68-67-73-70, Ryan Palmer 70-70-67-71, Kevin Streelman 68-68-72-70
279 - Jonas Blixt (SWE) 70-71-68-70, Daniel Chopra (SWE) 69-67-70-73, Scott Dunlap 72-68-68-71, Harris English 68-67-73-71, Matt Jones (AUS) 71-64-73-71, Sean O'Hair 73-68-67-71, Henrik Stenson (SWE) 68-67-71-73, Daniel Summerhays 71-71-68-69, Brendon de Jonge (ZIM) 69-68-70-72
