The Bretagne-Schuller rider made a decisive move 1.2km from the end of the 62nd edition of the race that saw the riders travel 190.9km.
French champion Nacer Bouhanni and John Degenkolb, a winner of five stages at the Vuelta a Espana, had to be content with second and third as 27-year-old Vachon picked up his third win of the year.
"Against them (Bouhanni and Degenkolb), I had no chance," said Vachon.
"There were five of my team in the lead group. They were at the front and I went with 1200 meters to go before a series of turns that I knew. The sprinters' trains were not in place and I took advantage."
Gregor Gazvoda (AG2R), Michael Morkov (Saxo Bank-Tinkoff Bank) and Preben Van Hecke (Topsport Vlaanderen-Mercator) were involved in the break of the day and had a 5:20 lead after 65km.
Slovenian Gazvoda was dropped inside the final 80km but the Dane and Belgian persisted with their break and were eventually joined by Jakob Fuglsang (RadioShack-Nissan) and Gael Malacarne (Bretagne-Schuller) with 25km remaining.
But they were caught with 4km left on the long, straight and largely downhill run into Bourges by a 28-man chase group.
A sprint finish looked inevitable but Vachon's perfectly timed move saw him follow up on his early-season wins at the Classic Loire Atlantique and Critérium International.