The Blues suffered a shock 2-1 loss to Basel at Stamford Bridge in their opening game to immediately complicate their bid to go through.
But a Fernando Torres double, plus a late Eden Hazard strike, secured a battling victory to send Chelsea ahead of their rivals and to the top of Group E.
It followed a 4-0 win at Steaua Bucharest last time out and Mourinho believes his side are now in the box seat.
"I told players after match against Basel we did garbage and we have to clean it," he told Sky Sports 2.
"We did it in the best possible way - two away wins and leading the group.
"We now have two matches at home. We are in a good position to qualify."
Mourinho was reluctant to single out the performance of Torres, who could have had a hat-trick after crashing a header off the crossbar.
Instead the Portuguese believes, after Samuel Eto'o scored his first Chelsea goal in the weekend 4-1 win over Cardiff, that his strikers are starting to fire.
"I prefer to say we have strikers who can work for the team and can also score goals," he said.
"Them (Torres and Eto'o) and Demba (Ba) are players with enough quality to play for us and succeed for us."
Speaking of Torres, he added: "He's a hard worker. He's not someone who hangs behind the fee Chelsea paid for him."
Mourinho also added that he does not plan to contest the Football Association's charge of improper conduct following his dismissal against Cardiff in the Premier League.
The Portuguese was sent to the stands by referee Anthony Taylor during the Blues' controversial 4-1 win at Stamford Bridge and was hit with the charge and given three days to respond on Monday.
The Chelsea boss said: "What the referee wrote is true. I was not aggressive, I was not offensive. I just had a disagreement.
"That in the game is resolved with 'shut up and sit down', (you) don't need to go to the stands.
"I accept the fine and against Manchester City (on Sunday) I can work."