A long-time breakaway group of five were together entering the final few hundred metres of the 200km course on The Mall but 24-year-old Blythe of the lowly NFTO team blasted out from the back, catching his favoured rivals cold.
He had enough power to hold off fellow Briton Ben Swift of Team Sky and Omega Pharma-Quick Step's Julian Alaphilippe.
Torrential rain left the course puddle-strewn and some of the riders failed to stay upright in the early stages as the treacherous conditions and narrow country lanes took their toll.
But as the route, much of which was used during the London 2012 Olympic Games, dried out, an 11-man breakaway took place that included 2012 world road race champion Philippe Gilbert.
That was trimmed to five to set up a superb finale as the main peloton, including 2012 Tour de France winner Bradley Wiggins, was unable to pull the breakaway group back.
The race completed a memorable weekend of cycling in the capital, which earlier in the day featured 24,000 amateur riders tackling a sportive over much of the same course after Saturday's freecycle event where 55,000 riders enjoyed 10 miles of traffic-free roads in the centre of the city.
In a high-quality women's grand prix race on Saturday Italy's Giorgia Bronzini beat hot favourite and 2012 Olympic road race champion Marianne Vos in the final few metres.
(Editing by Mitch Phillips)
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