Going into Tuesday night's home leg 3-1 down, few gave the Blues hope of turning the tie around against the star-studded French champions, but Demba Ba's late strike secured an unlikely 2-0 victory.
And Eto'o, who played a crucial part in the win on his return to the side, praised his manager for giving the players the belief that they could do it.
"It's incredible," Eto'o told The Sun.
"Mourinho had been telling us from the morning of the game that we could win the tie, and we knew it would be possible."
"He designed this incredible scenario for us. This is part of the magic of football."
After Andre Schurrle's first-half goal, a crucial second looked like it would evade the Premier League title chasers, with the woodwork twice denying them.
However, the Blues kept plugging away and got their reward, and Eto'o revealed it was all part of the plan.
"He (Mourinho) told us not to fall into the trap of being in too much of a hurry," Eto'o added.
"He said that we would get a goal in the first half and then score another at the end of the match."