'I knew I had it in me to win, but it's so hard to win out here,' said Bowden. 'It's almost surreal.'
Chris Couch fired a 6-under 65 to finish second. He ended 72 holes at 13-under-par 271, with Ryan Palmer and Bo Van Pelt one stroke back at minus-12. Jason Dufner and Dave Schreyer shared fifth place at 11-under-par 273.
Bowden, who opened the day with a three-stroke lead, quickly extended that as he birdied each of the first two holes. He later birdied the fifth to climb to 17 under.
However, he faltered to his first bogey of the day at the par-4 sixth. He stumbled to another bogey on No. 11 at Miccosukee Golf & Country Club to drop back to 15 under.
Bowden, whose last win came at the 1998 Miami Valley Open, erased that mistake with a birdie at the 12th. Heading to the clubhouse leading by three, the emotional Bowden bogeyed the 15th and 18th to win by one stroke instead of three.
'It's probably the most emotional day of my career,' Bowden said. 'With all that's going on with my father-in-law battling lung and liver cancer, and being 53rd on the money list and trying to keep my job. It's been rough.'
The win, along with the $90,000 first-place paycheck, moves the 35-year-old Bowden to No. 18 on the Nationwide Tour money list, with the top 20 automatically gaining their PGA Tour card for next season.
Couch entered the round in a tie for 13th place. He climbed the leaderboard with back-to-back birdies from the third and again from the eighth to climb to 11 under.
Around the turn, Couch stumbled to his lone bogey at the 10th. He rebounded with birdies on the 12th and 14th, and then capped his round with a birdie at the par-3 17th that gave him second place.
The more important thing for Couch is that he secures his PGA Tour card for next season, as he climbed to No. 9 on the Nationwide Tour money list.
'Last year was the worst year of my life,' said Couch, who struggled to finish 108th on the money list last year. 'I heard a lot of comments out here that 'Couch can't play anymore.' I was focused to prove everyone wrong this year. I'm glad it's over. This is so stressful. It's a great feeling. A big sigh of relief.'
Kelly Gibson, Blaine McCallister, Ted Purdy and Jason Schultz shared seventh place at 10-under-par 274. Barry Cheesman, Paul Claxton and Jeff Freeman finished another stroke back at minus-9.