Starting for the first time since returning to Stamford Bridge, Chelsea striker Drogba endured a frustrating evening as the Germans held on for a 1-1 draw in Group G.
He was unable to convert passes from Willian and Eden Hazard as Chelsea struggled to follow up their 100 per cent start to the Premier League campaign.
It seems certain Diego Costa, who missed out on Wednesday due to a muscle issue, will reclaim his place against Manchester City on Sunday.
But Mourinho was suitably impressed with Drogba, telling reporters: "He had a positive game. I'm not disappointed with the striker because of one inch, he scores a goal or doesn’t score a goal.
"I am happy with what he did. If he scores that goal in this moment we're speaking about 2-0, not 1-1. We had very good chances to score the 2-0 and we didn't.
"After the 1-1 we had a fantastic reaction and chances to win the game, but that's football, that's Champions League, that's normal.
"Congratulations to them because they got their objective. Yes a little bit of frustration for us, because we did everything to win and we couldn't."