Bowden closed with an 8-under 63 to get into the clubhouse at 16-under-par 269. Daley, the third-round leader, birdied the 18th hole at Glenmaura National Golf Club to shoot 1-under 70 and force the playoff.
In the extra session, Daley knocked his second shot over the green, while Bowden found the putting surface. Daley pitched on, but missed his par putt.
Bowden calmly two-putted for par to claim his third Nationwide Tour crown.
'It was one of those days where you can't really draw it up any better than that,' said Bowden, who collected $85,500 for the win. 'That's what your ideal day is, to come out here and shoot 63 in the final round and try to make a move.'
Brad Adamonis closed with a 2-under 69, his fourth round in the 60s to end in a tie for third at minus-15. Bryce Molder posted a 4-under 67 to join Adamonis in third.
Franklin Langham (65), Jay Williamson (68) and Brendon De Jonge (69) ended two strokes further back at 13-under-par 271.
Bowden got on the board with a birdie on the par-4 third. He chipped in for eagle on the sixth to jump to 11 under. Bowden posted back-to-back birdies from the ninth.
The 38-year-old moved to 14 under with a birdie at 13. Bowden gave that stroke back though as he three-putted for bogey on the par-three 15th.
Bowden atoned in a big way for that mistake as he holed a sand-wedge from 101 yards out for eagle on the par-4 17th. He came right back to birdie the last from 15 feet out to get in at minus-16.
'I just stayed patient today. I kind of thought I knocked myself out of it with the three-putt on 15,' admitted Bowden. 'I hit a lot of quality golf shots. I chipped in on six and obviously that got me going and then holed it on 17 from 101 yards. It was just one of those days.'
Daley was going good early with birdies on one and two that got him to 17 under. However, he bogeyed the fourth, then gave shots back at eight and nine to turn in minus-14.
The 28-year-old righted the ship with a birdie on 10, but gave that stroke right back with a bogey on 11. Daley turned it on late with birdies on 17 and 18 to force the playoff.
Stephen Marino carded his second straight 4-under 67 to end in a tie for eighth at 12-under-par 272. He finished alongside Richard Johnson (70) and Boo Weekley (71). Scott Dunlap and Tom Scherrer each fired 6-under 65s to share 11th place with three others.