The German was assured after the heated qualifying session on Saturday, and Hamilton's challenge in the later laps faded after he complained of having something in his eye impairing his vision.
Daniel Ricciardo put in another polished drive to take third place.
Further down the grid there was joy for Marussia, who through Jules Bianchi picked up the first championship points of their history when he claimed ninth place.
But it was another weekend for defending champion Sebastian Vettel to forget—the German's Red Bull lost all its power early in the race and he had to retire shortly after the first safety car had pulled in.
There were two safety car incidents—the first triggered early by Sergio Perez's accident, the second when Adrian Sutil's race came to an abrupt halt after some fine overtaking moves.
There were strong points finishes for Fernando Alonso, Nico Hulkenberg and Jenson Button, but the talking point will inevitably be the title race.
There was limited drama between the two on track in Monaco, but the storylines off the road are dominating the championship this season.
The drivers next head to Canada in two weeks' time.