The pair broke away from the field with 24 kilometres remaining with Mathias Frank, who had to settle for third place.
“If I wanted to win, I had to improvise,” said Bakelants.
“I knew that guys like Philippe Gilbert or Greg Van Avermaet would be hard to beat in the sprint. That’s why I attacked earlier.
“Because of the bad weather I knew that the peloton would not go faster than the break in that rain.”
It was Bakelants’s fourth win of an impressive season which also saw him don the yellow jersey at the Tour de France in July after winning the second stage.