Chad Collins bogeyed the 71st hole to fall one shot short of a potential playoff. He carded his third straight 68 to end at 11-under-par 273.
Cliff Kresge (68) and third-round leader Franklin Langham (70) shared third place at minus-10. Chris Smith fired a 5-under 66 in the final round to end at 9-under-par 275. He was joined there by first-round co-leader Matt Weibring (68).
Wagner got off to a hot start with back-to-back birdies to move into a share of the lead at minus-10. He gave away a stroke at the third to fall one back.
The 26-year-old moved back into a share of the lead at minus-10 with a birdie on the fifth at Le Triomphe Golf & Country Club. Collins and Langham also birdied the fifth to pull one ahead.
Wagner birdied the seventh, but gave a stroke back at the next to fall two behind Collins. A birdie on the 11th got Wagner back into a tie for the lead at minus-11.
The former Virginia Tech standout cruised to six consecutive pars from there and headed to the last hole one behind Collins. Wagner drained an 8-foot birdie there to move to 12 under. Then he had to wait and watch the final pairing finish.
'There's going to be a playoff,' Wagner said to his fiancee while watching. Then answering a spectators question about watching the last group finish, Wagner said, 'No, it's not fun.'
Collins, playing one group behind Wagner, bogeyed the 17th to drop to 11 under. He could only par the last to finish one back.
The 27-year-old had opened with birdies on one and two to join Langham and Wagner in the lead. Collins birdied the fifth to keep his share of the lead. He moved one clear of the field with a birdie at the seventh.
The 2005 Henrico County Open winner faltered with a bogey on the ninth, though. Collins pulled one ahead with a birdie on the 14th, but he could not hang on down the stretch. His 20-foot birdie effort at the last slid by the right edge and the win was Wagner's.
'Like I said, this was a long time coming, but I felt like I could do it,' said Wagner who collected $90,000 for the win. 'I was nervous all day, and I was wondering if I could make it around the whole course, but my caddie (Hale) kept me focused and I did it.
'It has taken me a while at every level. But once I won I was able to get on a roll. Maybe I'll rattle off a couple of more and get a battlefield promotion.'
Langham opened with birdies on one and five to move to 11 under and maintain a share of the lead. However, he ran off 12 straight pars before a three-putt bogey on the last dropped him into a share of third.
Bob Heintz closed with a 67 to take seventh place at 8-under-par 276. Scott Gutschewski was two strokes further back at minus-6 after carding a 6-under 65, which was the low round of the day. Craig Kanada, Jeff Klauk, Deane Pappas, Phil Tataurangi and David Edwards shared ninth place at 5-under-par 279.