Spurs were knocked out of the competition by Julian Nagelsmann’s men, losing 3-0 on the night in Germany and 4-0 on aggregate.
Following a recent slump in form, the North Londoners are now seven points adrift of the top four in the Premier League and face a resurgent Manchester United side on Sunday.
In an interview with the media after his side’s exit from Europe’s premier club competition, Mourinho said Tottenham will struggle to finish in the top four.
“With the squad we have at the moment it is going to be very, very difficult,” the former Chelsea boss said.
“Our problems are not going to disappear tomorrow.”
“Every team in the world would struggle with five or six of their most important players missing. It's as simple as that.”
“So that's a big problem. I know our team will automatically improve next season with these players back but we know we have to improve in other areas.”
“I will not tell you exactly. But the first and second goals we conceded I saw the mistakes and I saw why we made them and why their defenders were dominant.”
“We have problems and they don't end with the injuries but no team in the world can cope with such injuries for such a long time.”
“Mentally the players try to renew their motivations and they will give everything next time but not easy for them.”