Mile Svilar saved a penalty for Benfica, though was eventually beaten twice in the Champions League defeat.
United keeper David de Gea, meanwhile, pulled off vital saves either side of half-time to deny Diogo Goncalves.
Afterwards, Mourinho revealed: "The words that I exchanged were quite relaxed.
"When their keeper made the penalty save I just smiled and said to him you have a keeper for many years and when De Gea made a good save he said similar, kind words, that De Gea was not bad either."
Svilar had an own goal attributed to him after Nemanja Matic's effort bounced off his back and behind the goalline.