Anthony Gordon gave Newcastle a 1-0 lead before Harvey Barnes struck twice after the break.
Mourinho said afterwards: "In the first half, it was a quiet St. James' Park. (The home fans) felt Benfica were much closer to scoring. (Newcastle) brought their enthusiasm from set pieces.
"That was the only moment when they put pressure on their opponents. In the second half, the second goal killed the game.
"(It was) a good performance in the first half. It's not easy to come here and play the way we did in the first half, creating four big chances, hitting the post, being the team that – in my opinion – was closer to winning.
"(We have) 15 points to play for with three matches at home. We lost to Chelsea away, Newcastle away, which in the end wouldn't be dramatic. I would say maybe ten, 11 are the points we need to qualify, so game on."