Thompson finished at 16-under 268, good enough for a two-shot win after Burns bogeyed the 18th hole. It was Thompson's first win in six chances as the 54- hole leader on the Nationwide Tour.
'It is hard to put into words,' said Thompson, who claimed $81,000 for the win. 'It has always been a dream of mine to win on the Nationwide Tour. To finally get this win is huge.'
Burns took a penalty on the final hole and made bogey when a birdie could have sent the tournament into a playoff.
Looking for his third Nationwide Tour win and first since 1998, the onetime PGA Tour winner closed with a 3-under 68 to take second place alone at 14-under 270.
'I had risk or reward on that last shot,' said Burns, who went for the green with a 5-wood from 240 yards out at the 18th, putting it into the water.
'I had second place wrapped up. But from the tenth hole on, I knew if I got close I was going for it on the last hole.'
Rick Price had a 4-under 67 and finished in third place at 12-under 272.
Garrett Willis shot the round of the day by two strokes with a bogey-free, 7-under 64 that vaulted him from a tie for 26th place overnight into fourth place at 11-under 273.
Marc Turnesa (67), D.A. Points (67) and Tommy Biershenk (69) shared fifth place one shot further back at 274.
Thompson opened with rounds of 64 and 65 this week, then cooled off on the weekend with a 69-70. He came within two shots of tying the tournament scoring record.
Prior to this week, his best finish this season was a tie for fifth place at the Melwood Prince George's County Open last month.
'I wouldn't say it has been a struggle, but it has been a journey to get to this point and finally win,' said Thompson, who was making his 120th career Tour start. 'Every time I've been in contention I've played pretty solid, but I've never had that five- or 6-under round to finish up with.'
Sunday, he didn't either. But 70 was good enough.