Marcus Rashford broke the deadlock midway through the second half when an inswinging free-kick from the left was carried over his line by teenage goalkeeper Mile Svilar.
Svilar, who became the youngest goalkeeper to start a Champions League game aged just 18 years and 52 days, caught the ball but in doing so stepped backwards over his line to gift United the lead.
It was a lucky break for the Premier League high-flyers, who, despite dominating possession, had been struggling to create meaningful chances against the Portuguese champions, twice winners of the European Cup.
Benfica showed increased urgency after going behind, bringing on forward Jonas for Diogo Goncalves, but they failed to trouble David de Gea in the visitors’ goal.
Rashford limped off with about 15 minutes to go, replaced by Anthony Martial, who tested Svilar early following an incisive run into the box.
Benfica captain Luisao was sent off in added time after a lunge at United substitute Scott McTominay to compound the home side’s misery.
Upbeat United manager Jose Mourinho said his side were in control of the match throughout.
“I never felt that we could concede a goal,” he said.” We were very solid defensively. Sometimes I feel to be good defensively is a crime but it is not a crime.
– Defensive solidity –
“To be good defensively is one step to get results and we have nine points. We are basically I think one point away from qualifying and one victory away from winning the group so we are fine.”
He said United had discussed how to put pressure on the young goalkeeper at set-pieces, including putting players around him on corners to chip away at his confidence.
Mourinho made four changes to the team that started Saturday’s cagey 0-0 draw with Liverpool in the Premier League, with former Benfica player Victor Lindelof, Daley Blind, Juan Mata and Rashford returning to the side.
But it was Benfica who played the more enterprising football in the early stages as the visitors struggled to establish any rhythm and were frequently caught offside as they tried to make inroads.
United, unbeaten since they lost the European Super Cup to Real Madrid in early August, have made an impressive start to the season, scoring freely before the weekend’s Anfield stalemate.
But defensively the three-time European champions have also been solid, conceding just six goals in 13 games in all competitions.
Svilar beat Iker Casillas’s record — the Real Madrid legend made his debut in the competition in 1999 at the age of 18 years and 118 days.
United, who did not qualify for the Champions League last season, now have nine points out of nine in Group A and look almost certain to qualify for the knockout stages but Benfica, without a single point, have a mountain to climb.
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