After smashing into John Terry, the Spaniard was forced off early in the second half of the game, which the Blues won in extra-time courtesy of Branislav Ivanovic's header.
Fabregas slid in to try and clear the ball five minutes into the second half of Tuesday's clash at Stamford Bridge but collided with his captain, who had committed to the challenge from the opposite direction.
Mourinho immediately took the decision to substitute Fabregas in favour of Ramires with Saturday's Premier League crunch clash against title rivals Manchester City looming large on the horizon.
And when quizzed over Fabregas, as well Filipe Luis who was also taken off due to injury, the Portuguese coach told reporters: "Filipe was a calf and Fabregas was a hamstring.
"Fabregas told me he wasn't injured immediately after clashing with Terry, but that he would be in a few moments."
Fabregas has made 21 Premier League appearances for Chelsea this season, notching two goals and 15 assists.
