Brazilian Anderson Talisca, 20, put Benfica ahead after two minutes with his seventh goal this term but Braga levelled when Eder finished off a counter-attack before the half-hour.
Salvador Agra got Braga's winner in the 81st minute and they held on despite having Danilo sent off in stoppage time.
Benfica, with 19 points from eight games, saw their lead cut to one point after rivals Porto won 5-0 at Arouca on Saturday
Porto's Colombia forward Jackson Martinez scored twice, while his compatriot Juan Quintero, Casemiro and Vincent Aboubakar shared the other goals.
Vitoria Guimaraes are third with 17 points after Joao Afonso gave them a 1-0 win at Vitoria Setubal on Friday.
Fourth-placed Sporting Lisbon, on 16 points, bounced back from their controversial Champions League loss to Schalke 04 to beat Maritimo 4-2, having stormed to a 3-0 halftime lead.
Patrick Bauer diverted Andre Carillo's cross into his own goal after eight minutes, Joao Mario turned in Nani's low cross after 15 minutes and Paulo Oliveira headed home a Nani corner just before halftime.
Maritimo's Niger forward Moussa Maazou scored twice in five minutes early in the second half, taking his league tally to seven, to pull the Madeira side back into the game.
But Colombia forward Fredy Monteiro gave Sporting some breathing space when he controlled Adrien's pass on his chest and scored with a shot on the turn.
"We had losses of concentration which we cannot afford to have and which allowed Maritimo to score two goals," said Sporting coach Marco Silva.
"It's a lesson for us, we can't go to sleep when we have a comfortable advantage.
(Writing by Brian Homewood; editing by Ken Ferris)
