He was spotted leaving Old Trafford on crutches after his team-mates had secured a comfortable 3-0 victory over the Swiss side thanks to goals from Marouane Fellaini, Romelu Lukaku and another landmark Marcus Rashford strike.
And things have got worse following confirmation that they have been hit by a charge from European football's governing body.
"Charges against FC Basel 1893: Setting off fireworks - Art. 16 (2) of the UEFA Disciplinary Regulations (DR)".
Pogba should also miss United's match against CSKA Moscow in the next game of their Champions League campaign, while Mourinho's side also have to see off Burton Albion in the next round of the League Cup.
However it was the hosts' night and the Red Devils did have more opportunities to add to the scoreline, particularly in the first half with Henrikh Mkhitaryan missing two great chances, including hitting the post from close range. We don't cry. No Paul for Sunday.
Lukaku headed home Daley Blind's cross at the far post to notch his first goal in the group stages of Europe's elite competition - he scored three times in the Champions League qualifiers as a youngster playing for Anderlecht.
On Fellaini, in particular, Mourinho added: "He is a player with special qualities who does things that some other players can not do".
Mourinho's other concern was a hamstring injury that forced Paul Pogba, United's skipper, off midway through the first half.
Zlatan Ibrahimovic was named in Manchester United's Champions League squad but its doubtful whether he will play as he is recovering from an ongoing injury.
"I am always ready to play", Herrera said.
Lindelof does not expect Paul Pogba's absence to prove too much of a problem either.
"He is a player with special qualities, and he gives me multiple areas of action".
"The only match we made a decision to play with three [Herrera] played, today we went back to two again".