Mourinho also criticised what he perceived to be a viewpoint that "being good defensively is a crime" and insisted that he knew Man United would eventually break Benfica's resistance.
"We were in control, David de Gea did not have one save to make. I never felt we could concede a goal and were solid defensively," Mourinho told reporters following the game at the Estadio da Luz.
"Sometimes I feel being good defensively is a crime, but that is a way of getting results. We are one point from qualifying and one victory away from winning the group with two games at home to play. A good game, solid.
"I knew how good the goalkeeper was, I told the players that. We had a little bit of a strategy, especially on set-pieces to make him uncomfortable. We put men around him on corners so he cannot come out. He risks a lot, but only top keepers do that. He was unlucky for the goal.
"We knew the Benfica pressure could not stay for 90 minutes. The amazing defensive work Liverpool did against us, Benfica could not do that for the whole game. Without any pressure, we knew the goal would arrive. We forced a little more and with quality and sharpness we could have killed the game more."
United top Group A after winning all three games, while Basel beat CSKA Moscow 2-0 in the other group fixture of the night.