With the Carling Cup already in the trophy cabinet and the Premiership title just three wins away, Mourinho will want nothing to disrupt their challenge for Europe's premier prize.
Watching on the TV in his hotel room here last night, he was disappointed by the way his team conceded two goals in the last five minutes.
Didier Drogba's header in the 80th minute, which gave Chelsea 2-1 lead on the night, 6-3 on aggregate, had sent thousands of Bayern fans streaming home and rendered the tie all but over.
Why Chelsea suddenly lost their focus when the match appeared won is a question Mourinho is bound to address with his coaching staff not only because of the injury to Terry.
The England centre-half and Portugal's Ricardo Carvalho had been central figures in the first half in denying Bayern the single goal that might have swung the tie back in their favour.
The speed with which Carvalho intercepted balls on the ground and the power with which he challenged for them in the air gave Bayern's first choice strike partnership of Roy Makaay and Claudio Pizarro little scope in their search for an early goal.
Unusually, the service to them was predictable and seemed to bring the best out of Carvalho and Terry. On the one occasion that Ze Roberto beat Robert Huth and supplied a cross that was actually dangerous, Petr Cech was equal to Pizarro's close range shot.
And, in the 30th minute, Chelsea took the lead. On a rare foray forward, Joe Cole skipped across the Bayern penalty area and set up a chance for Frank Lampard.
A specialist at attacking the ball late from midfield, Lampard surged forward and hit a low drive that struck Lucio, wrong- footing Oliver Kahn. The Bayern goalkeeper dived to his right but watched Lampard's shot nestle in the opposite corner.
Still Bayern seemed unable to raise their game, though Michael Ballack missed a wonderful chance to equalise just before the interval when he lifted a shot yards over the bar from about 10 yards.
It wasn't until Bayern introduced 34-year-old substitute Mehmet Scholl, a Champions League winner in 2001, that the Germans began to present Chelsea with problems. He immediately set up a chance for Ballack that was wasted, emphasising the difference between the teams.
Chelsea created far fewer chances but did more with them. A Lampard free-kick, for instance, resulted in Damien Duff forcing a brilliant close range save from Kahn.
Finally, in the 65th minute, Bayern hit the target. Cech turned Ballack's header onto a post but the ball ran across goal to Pizarro who scored easily.
Then Bixente Lizarazu hit the bar and the industrious Eider Gudjohnsen cleared off the line from Ballack, but this fresh enthusiasm
hadn't reached the German defenders.
They seemed disinterested when Cole collected the ball out on the left. He casually picked out Drogba who forced his way in front of Robert Kovac and steered his header beyond Kahn.
With 10 minutes remaining, the match seemed over.
Then Terry was hurt and, in the 90th minute, substitute Paolo Guerrero took advantage of the disarray in the Chelsea defence to turn in Bastian Schweinsteiger's driven cross. Five minutes into added time, Scholl scored again and suddenly the Chelsea bench were screaming for the final whistle.
For Chelsea, it was a demeaning end to a trip that, off the field, did little to enhance the club's reputation. But that shouldn't be allowed to diminish the achievements of the team.
They now face Juventus or Liverpool, who start tonight's second leg leading 2-1. It's not hard to guess who Chelsea will prefer.
They've defeated Liverpool three times this season while Juventus have twice beaten Bayern Munich 1-0 in the Champions League this season.
