For the first time in Nationwide Tour history, play was spread throughout three courses - The Cliffs Valley Course at the Cliffs Golf & Country Club, The Cliffs at Keowee Vineyards and The Cliffs at Walnut Cove. The Cliffs Valley Course is a par-72 layout, while the other two are par 71s.
Bertsch began the day 12 behind Australia's Mathew Goggin, but Bertsch was playing the easiest course in the rotation on Sunday, the Cliffs Valley Course.
He opened with a bogey at the second hole, but he closed his front nine with four birdies to make the turn at 3-under 33. Bertsch birdied the 10th to get near the top of the leaderboard, but back-to-back birdies from the 14th put him into a tie for the lead with Watson, who was in the clubhouse at minus-11.
Bertsch ran home an 18-foot birdie putt at the last hole to go up by one at 12-under par.
Bertsch had to wait as Hoffman was still on the course, the Walnut Cove track. He was 4 under par on his round and his birdie at the sixth, his 15th on Sunday, tied him with Bertsch.
Unfortunately, Hoffman double-bogeyed No. 7 and fell two back. He birdied the eighth, but when he failed to birdie No. 9, Bertsch was on his way to the winner's circle.
'This feels so good,' said Bertsch, who pocketed $112,500 and moved up to second on the money list. 'It is a weird game. If you would have seen me on Tuesday you would have said there is no way this guy can win here.
'It was such a weird situation with the wind blowing like it was and with us on three different courses. The key for me was doing a good job of staying in the moment and focusing on the task at hand.'
The win was Bertsch's second on the Nationwide Tour. He titled at this event in 2000 when it was named the Buy.com Upstate Classic.
Hoffman finished with a 3-under 68 on Sunday, while Watson, who played Cliffs Valley, shot a 1-under 71.
Kyle Thompson (70), Tim O'Neal (69) and Roger Tambellini (68) tied for fourth place at 9-under-par 205. Jeff Klauk carded a 5-under 67 and took eighth at minus-eight.
Goggin struggled to a 5-over 76 and tied for ninth with Jim McGovern (71), Tim Wilkinson (68), Matt Weibring (72) and Chris Wollman (70). The group came in at 7-under-par 207.