The Ivory Coast striker, who returned to Stamford Bridge this past summer, replaced the injured Loic Remy in the 16th minute before converting from the penalty spot in the 23rd minute as the Blues hammered the Slovenians 6-0.
It was Drogba's first goal since rejoining the west London club and 158th in total and his performance was praised by Mourinho who was not expecting him to be involved so heavily.
"I was not expecting him to play 75 (minutes)," Mourinho said.
"I spoke with him yesterday and we spoke about 30. Circumstances. He had to go on.
"He was comfortable to play 75 minutes. It was very, very important for Didier. The best thing for a player to improve his condition is to play.
"His last goal for Chelsea was the most important goal in the history of the club (in the Champions League final in 2012). So to be back and to score again at Stamford Bridge is nice for him. Good."
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