The German champions were held to a goalless draw in the opening half at the Estádio da Luz, but three goals in the final 17 minutes earned José Barcala’s side all three points.
Bayern controlled much of the first half but struggled to break down a disciplined Benfica defence. Goalkeeper Ena Mahmutovic was also called into action, making important saves to keep the visitors level.
Benfica continued to frustrate Bayern after the interval, but the breakthrough finally arrived in the 74th minute.
Klara Bühl collected the ball following a Benfica goal kick, skipped past a defender and unleashed a powerful effort from the edge of the penalty area. Her strike went in off the inside of the post to give Bayern the lead.
Bayern doubled their advantage six minutes later when Pernille Harder reacted quickest inside the penalty area to sweep the ball into the net.
The goal was particularly significant for the Denmark international, as it was her 50th in the Women's Champions League and Women's Cup, making her only the fourth player to reach the landmark.
Franziska Kett completed the scoring in the 88th minute after starting a counter-attack and exchanging passes with Bühl before finishing from inside the area.
Goals
• Benfica: No goals.
• Bayern Munich: Klara Bühl 74', Pernille Harder 80', Franziska Kett 88'.
The victory gives Bayern their first three points of the league phase after their opening 2–2 draw against Manchester City.
Bayern will next face Real Madrid at home on 28 October, while their league campaign also includes fixtures against Paris Saint-Germain, Austria Wien and defending champions Barcelona.