Armitstead took the two-up sprint in a photo finish with Swedish rider Emma Johansson (Wiggle-High5). Armitstead's team-mate Chantal Blaak placed third.
Armitstead and Johansson had broken clear of a lead group heading into the final climb of Paterberg, with nine riders left to chase them down.
Heading under the kilometre-to-go banner Armistead and Johansson became wary of each other's tactics, with neither wanting to lead out the other in the final sprint.
>>> Lizzie Armitstead: I went to London to get a top 10 but I’m going to Rio for gold
With the chase group being paced up quickly by Frenchwoman Pauline Ferrand-Prevot (Rabo-Liv) behind them, their hand was forced and the pair had to engage in a long sprint.
Armitstead has already won the Omloop Het Nieuwsblad, Strade Bianche and Trofeo Alfredo Binda this year. It's the first time that she has won the women's Tour of Flanders - now part of the UCI's inaugural Women's WorldTour.
The women's route took in 141km, and featured 10 categorised climbs and five sectors of cobbled roads.
Armitstead now returns to the top of the Women's WorldTour ranking, with Blaak in second and Johansson in third.
Watch: Women's WorldTour contenders 2016
Women's Tour of Flanders 2016, 141km
1. Lizzie Armitstead (GBr) Boels-Dolmans
2. Emma Johansson (Swe) Wiggle-High5 at same time
3. Chantal Blaak (Ned) Boles-Dolmans at 4 secs
4. Megan Guarnier (USA) Boels-Dolmans
5. Elisa Longo Borghini (Ita) Wiggle-High5
6. Ellen Van Dijk (Ned) Boels-Dolmans
7. Annemiek Van Vleuten (Ned) Orica-AIS
8. Pauline Ferrand-Prevot (Rabo-Liv)
9. Claudia Lichtenberg (Ger) Lotto-Soudal
10. Katarzyna Niewiadoma (Pol) Rabo-Liv at same time
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