The Lisbon club's win means they extend their championship lead to 13 points over third-placed Braga and go three ahead of Porto, who host Gil Vicente on Monday.
Benfica started strongly, pressured Braga high up the pitch, and deservedly scored two first-half goals through Argentine Eduardo Salvio and Brazilian striker Lima.
Braga pulled one back when forward Joao Pedro struck with just a little more than 10 minutes on the clock but it was too late for the hosts who were dealt a further blow when central back Maximilian Haas was sent off.
It was the first time that Benfica coach Jorge Jesus had beaten Braga away since he took the job in 2009.
"We surprised Braga, scored two early goals and could have scored more. Later on we did well to know how to defend the result," Jesus told Portuguese television.