After 14 laps of a circuit taking in Regent Street, Trafalgar Square and Piccadilly Circus, the Mitchelton Scott rider timed his sprint to perfection to cross the line ahead of Germany's Andre Greipel and Colombian Fernando Gaviria.
Alaphilippe (Quick-Step Floors) finished safely in the peloton in the 77km finale watched by large crowds.
Team Sky's Wout Poels, winner of Friday's stage in the Lake District, finished second overall with green jersey leader Primoz Roglic completing the podium.
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(Reporting by Martyn Herman, editing by Ed Osmond)
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