The Briton, who rides for the Sky team, completed the course in 4 hours 49 minutes and 54 seconds. He finished ahead of Belgium's Greg Van Avermaet and Edvald Boasson Hagen of Norway, a teammate of Stannard's.
The race ended in a sprint between the Fleming and the Briton. "I waited until he was looking the other way" Stannard told newsmen. "I often perform well in bad weather, but really all you need to do is wrap up well."
Belgium's Sep Vanmarcke, who won this event in 2012, was 4th.