After 14 laps of a 77km 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 Andre Greipel (Lotto Soudal) and Fernando Gaviria (Quick0-Step Floors) and claim a victory in his last race wearing Mitchelton-Scott colours.
"This year hasn't been great for me so I really wanted to finish off with a good result," Ewan said. "I was so motivated to win this stage and I am just happy I had the strength and legs in the end.
"It was really hectic in the end and I was just lucky my team put me in perfect position. Not many guys had lead-outs in the end, I could pick the wheels that I wanted to be on and I had a really good run to the line and I felt really good as well.
"To finish off with a win means a lot to me and it gives me a bit of confidence."
After an active stage, the sprinters' teams controlled the closing kilometres to set up the much-anticipated bunch sprint on the uphill finish line on Regent Street.
Mitchelton-Scott's riders were in formation towards the front end of the strung-out peloton before another Australian, stage two winner Cameron Meyer, helped move Ewan up to the front with just 1.5km remaining.
Roger Kluge then took over and powered down the final straight to allow Ewan to launch his winning burst, making it a stage victory in each of the past three editions of the British race for the 24-year-old.
Alaphilippe (Quick-Step Floors) finished safely in the peloton in the 77km finale watched by large crowds.
"I'm really, really happy, and proud to have this new result on my palmares," Alaphilippe said. "I didn't expect that I would be able to win the overall classification in my first participation in this race.
"It was not an easy stage today; it was really fast so I was really focused until I crossed the line. Now I can be happy and proud to have won.
“To be quite sincere, I was surprised by my shape, because after the Tour de France I rode only San Sebastian and a couple of criteriums, so to see that I have such a good condition gives me a big boost of confidence for the remaining of the season and the next important races on my calendar."
Team Sky’s Wout Poels, winner of Friday’s stage in the Lake District, finished second overall with green jersey leader Primoz Roglic (LottoNL-Jumbo) completing the podium.