Pogba marked his first appearance for the Red Devils in over two months with a goal and an assist before he was replaced by Marouane Fellaini in the 70th minute of the 4-1 win over Newcastle.
Mourinho admitted that United had sorely missed Pogba's creativity during his injury absence and described the France international's performance against the Magpies as "different class".
"He looked like he wasn't out for such a long time without playing football," the United manager told MUTV.
"At the beginning of the season we had Paul and [Nemanja] Matic growing up together and being like the engine of the team. We lost a little bit of that; other players are good players but they have different qualities, so [it] was good.
"He affects our football. With him we have much more creation."
Mourinho said he was wary of playing Pogba against Basel in midweek and suggested that resting the France midfielder may be of benefit to United in the long run.
The Red Devils have won all four of their Champions League group games to date and only need a point from the remaining two fixtures to secure a place in the knockout stages.
"The best thing for him may be to play again, but the best decision may be to rest him because he is a player we need to protect," Mourinho said.
The Portuguese coach also expressed relief at Romelu Lukaku ending his seven-game goal drought for United, after the striker rifled in from Marcus Rashford's lay-off for United's fourth against Newcastle.
"It is not a problem for me if he works like he does and he doesn't score goals but, for the self-confidence, strikers love to score goals," Mourinho said.
"He was not doing that for us for a few matches and I know that can affect strikers' confidence, so I was really happy that he scored that goal."