Goals from Torres, Aguero and Sterling left no chance for the French club in the European Cup spring.
Manchester City hosted Marseille in the final round of the Champions League group stage.
The French missed three unanswered goals and ended the European Cup season, finishing fourth in their group.
Despite the fact that Porto dealt with Olympiacos in a parallel match, it is the Greek club that goes to the Europa League, not Marseille.
Fatal for the charges of Andre-Villas Boas was the missed goal in the home match with Olympiacos.
Manchester City 3-0 Marseille Goals: Ferran Torres, 48, Aguero, 77, Sterling, 90 Manchester City: Steffen - Walker, Garcia (Stones, 28), Laporte, Ake - Fernandinho, Gundogan (Sterling, 46) - Marez (.