After four wins from their opening four group games, United travelled to Switzerland needing just a point to qualify for the knockout phase.
United dominated the first half at St. Jakob-Park but were punished for failing to take their chances as Michael Lang breathed life into Basel’s qualification hopes with a dramatic late winner.
Lang’s 89th-minute winner means that United, Basle and CSKA Moscow can all finish on 12 points in Group A if the Russians win at Old Trafford next month.
However, CSKA would have to beat United by six goals, meaning that Mourinho’s side are almost certain to progress to the knockout stage despite losing their 100 per cent record.
‘Can you help me with the maths?’ said the United boss afterwards.
‘What do we need against CSKA? I don’t even think we need to draw. We can lose by some numbers and still go through.’
Mourinho was even more confused that United had managed to lose a game they dominated in the first half, making several clear chances and hitting the woodwork twice.
‘We lost because in the first half should be 5-0. We could not score one after being so dominant in such an easy way that it seemed impossible not to win,’ he added.
‘But if you miss so many chances you put yourself in this situation.
‘The first half was a perfect half without the goals, was perfect. It was difficult to repeat in the second half.
‘I think we play a match like this 10 times and nine we win comfortably. The one was now.’
Mourinho acknowledged that his team seemed to be settling for a goalless draw that would have taken them through as group winners when Basle struck.
He added: ‘The fact we knew one point is enough, probably we thought is not now our time to try to win and time to control and in the end we lost. But it’s hard for me to be upset with the players.’