The 25-year-old beat team-mate Alex Dowsett to the line with Russell Hampton (Raleigh-GAC) completing the podium.
With defending champion Bradley Wiggins, 2010 champion Geraint Thomas, Chris Froome, David Millar and Mark Cavendish all missing as they prepare for the Tour de France, a wide open race was expected.
The eventual top three plus Graham Briggs (Raleigh-GAC) and Oli Beckinsale (Endura MTB) escaped in the opening half of the 182km race and built up a lead of six minutes.
The second half of the race saw six 15km rolling circuits and Briggs and Beckinsale were dropped as the leaders saw their advantage cut by half.
But the peloton were unable to organise a sustained chase and with 40km left, the lead had ballooned out to seven minutes.
With 30km remaining, Stannard attacked and came home alone in the grounds of Ampleforth College
Sharon Laws scored a surprise victory in the women's race, rebounding from her Olympics omission to ride solo over the last 25km to beat Lizzie Armitstead by 96 seconds with Emma Pooley five seconds further back in third.
Ten time winner Nicole Cooke was sixth, over nine minutes back.
Other National Champions:
France: Nacer Bouhanni
Germany: Fabian Wegmann
Italy: Franco Pellizotti
Spain: Francisco Ventoso
Belgium: Tom Boonen
Netherlands: Niki Terpstra
Switzerland: Martin Kohler
Austria: Lukas Poestlberger
Luxembourg: Laurent Didier
Denmark: Sebastian Lander
Norway: Edvald Boasson Hagen
Slovakia: Peter Sagan
Czech Republic: Milan Kadlec
Slovenia: Borut Bozic
Russia: Eduard Vorganov
Ukraine: Andriy Hryvko
Kazakhstan: Assan Bazayev
Moldova: Alexandr Pliuschin
Estonia: Tanel Kangert
Latvia: Aleksejs Saramotins
Lithuania: Gediminas Bagdonas
Ireland: Matt Brammeier
Portugal: Manuel Antonio Cardoso
