Roger Tambellini carded a 67 to finish alone in second place at 11-under-par 202. Kelly Gibson was one shot further back at 10-under-par 203.
Bowden, who could use a victory this week to dramatically improve his standings on the money list, wasted no time at Miccosukee Golf & Country Club and picked up a birdie at the par-5 first.
The 35-year-old added another birdie at the par-5 seventh to make the turn at 10-under before taking control on the inward half.
'I drive it straight. I don't hit it very far, but I drive it straight,' said Bowden, who hit 13 of 14 fairways and 17 of 18 greens in regulation. 'If I drove it crooked and short, I'd be doing your job (referring to the golf writers he was speaking with).'
Bowden tallied back-to-back birdies from the 10th to surge into the lead and began to pull away from his challengers thanks to a birdie at the par-5 14th. Bowden then birdied the par-4 16th to pad his advantage going into the final round of the inaugural event.
'This course suits me. I drive it fairly straight and I keep it in play,' Bowden said. 'The greens are so small, if you hit it in the middle of the green you're going to have a decent putt at it.'
The Indiana native is in search of his first victory on the Nationwide Tour since the Miami Valley Open in 1998.
'I refuse to think about things I can't control,' said Bowden. 'I can't control the wind. I can't control the rain. I can't control who's doing what on the leaderboard. I'm going to stay aggressive, I have to.'
Tambellini, who earned his first career victory at the Albertsons Boise Open in September, collected two birdies and an eagle over his first nine holes.
The 28-year-old stumbled with a bogey at the 10th but managed a birdie at the par-three 17th to break a logjam for second place.
Paul Claxton, who held the lead heading into the weekend, struggled with a 2-over 73 on Saturday.
Claxton was joined by Chris Starkjohann, Ryan Palmer, Brett Wetterich, Grant Waite, Jason Dufner and Mark Hensby in a tie for fourth at 9-under-par 204.
Barry Cheesman and Jess Daley finished one shot further back at 8-under-par 205.