A listless display at City's Etihad Stadium, particularly in the first half, allowed Chelsea's main title rivals to steal a march and move five points clear.
But the tactics adopted by the Portuguese manager raised a few eyebrows.
Mourinho dropped a big bombshell when long-term captain and defensive colossus John Terry was substituted at halftime for tactical reasons -- the first time Mourinho had ever taken his trusty skipper off in the heat of battle.
Terry's position in the team will dominate the week ahead as Chelsea prepare to face West Bromwich Albion.
"I had to decide on John or (Gary) Cahill because Zouma is the fastest player we have in our defensive line," Mourinho explained of his decision to hook Terry.
"The point was not to bring John out but to bring Zouma in. I wanted to have my fastest player on the pitch.
"I'm the one that plays John every game, made him captain, brought him back from a difficult situation with other managers."