The hosts climbed to fourth in the table courtesy of first-half strikes from Carlitos and Evandro, with Raul Rusescu grabbing Braga's goal late on.
Jesualdo Ferreira's men, meanwhile, suffered just their second loss in seven top-flight games as the home side gained a measure of revenge for the 3-2 defeat they suffered in September's reverse fixture.
Carlitos set Estoril on their way after 24 minutes, producing a calm finish after collecting Javier Balboa's pass.
Evandro netted his ninth league goal of the season on the stroke of half-time to put them in the driving seat.
And that ensured that Rusescu's injury-time strike was nothing more than a consolation.
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