Flanagan ended the tournament at 10-under-par 270, one stroke clear of Driscoll, who coughed up a four-stroke lead in the final six holes. Driscoll closed with a 1-over 71 to finish at minus-9.
'My finish to last season wasn't that great so I worked hard in the off season. I wanted to come out and fulfill my potential,' said Flanagan, who picked up $108,000. 'I said to my caddie at Q School last December that I was going to come out here and win three. I guess I did it. It took until August, but I did it.'
The 23-year-old Flanagan earns an instant promotion to the PGA TOUR as this was his third win of the season. Earlier this year, he won the Henrico County Open and the BMW Charity Pro-Am at The Cliffs. In 2003, Jason Gore was the last to earn the Battlefield or three-win promotion.
With the FedEx Cup playoffs starting next week, the first PGA TOUR event Flanagan is eligible for is the Turning Stone Resort Championship, which takes place September 20-23.
'I guess I'll take some time off,' said Flanagan of his plans. 'I'm looking forward to getting out there and playing the rest of the year.'
Jason Day, who is No. 2 on the money list, closed with a 1-under 69. Day ended alone in third at minus-7while David McKenzie, Scott Parel and Justin Bolli were one shot further back at 6-under-par 274.
Driscoll was playing steady golf as he was 2-under for his round through 11 holes. The birdies he carded on the third and 11th moved him to 12-under par, four clear of Flanagan at Irondequoit Country Club.
Flanagan, who was playing three groups ahead of Driscoll, eagled the par-5 third to start his round. He rolled in a 7-footer for birdie on nine, then chipped in for birdie at 10 to move to 7 under.
The Australian birdied the 12th to get within three of Driscoll after his birdie at 11. The gap was down to two as Driscoll could not save par from a greenside bunker on the 13th.
Flanagan pulled within two strokes as he drained a 30-foot birdie try at 16. He parred the 17th, before converting a birdie putt from over 20 feet at the last to get in at 10 under.
With his group on the clock for slow play, Driscoll faltered on the 16th. He three-putted from the fringe for double-bogey to slide one behind Flanagan.
Driscoll knocked his second over the green at the 17th, but saved par from 18 feet. Needing birdie at the last for force a playoff, Driscoll dropped his approach 18 feet below the hole.
With Flanagan on the driving range staying loose, Driscoll's birdie putt came up short and right of the cup. He tapped in for par to finish second for the second time this season as Flanagan was congratulated on the range.
'I can't believe I won today that's for sure. I didn't think I could quite get there from seven back, but I shot seven-under and that is what I wanted to do,' Flanagan stated. 'I played average on the front nine and had that lucky shot on three and made eagle there, then had a good birdie on nine. I got lucky again on 10 and things just went right for me.'
David Mathis stumbled to a 2-over 72 Sunday to end alone in seventh at 5-under-par 275. Fran Quinn was one stroke further back at minus-4 after closing with 67.