The Nigerian, who took the captain's armband from Michael Essien in the second half, was the unlikely scorer of the Blues' first goal in the 66th minute before Oscar added a second five minutes later.
The performance of Mikel, who arrived at Stamford Bridge from Lyn in 2006 when Mourinho was last in charge, was met with adulation by the Portuguese.
"It was important for us, because we were dominating and dominating, creating and creating, but the goal was not arriving. It was like the winning goal," he said.
"He plays in a very intelligent and safe way. I never recognise his goalscoring appetite.
"For some reason Essien gave him the armband. Normally it should go to Ashley Cole. It made him believe that he was a goalscorer."
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