Bourgain was selected to compete in Saturday's race after French officials realized that, according to UCI rules, he had to represent his country in another competition at the Games to be entered in the keirin.
With no more spots available on the track, Bourgain was given a slot in the road race.
Bourgain dropped out as planned after three kilometres.
"I cannot do anything to help my fellow Frenchmen," Bourgain said. "Of course, it is a disadvantage for them to have me in their team, they will be only three."
French technical director Isabelle Gautheron told The Associated Press that Bourgain had to take the start and was not responsible for the controversy.
"He was right to apologize, he did the decent thing," Gautheron said. "But his best answer will be to win a medal in keirin."
Tour de France champion Bradley Wiggins criticized Bourgain's presence at the start, saying track cyclists' inexperience in big road races could even make them dangerous for other riders.