Goals from Gary Cahill and Diego Costa handed the Blues victory on Merseyside as they extended their unbeaten start to 17 games in all competitions.
However, Mourinho confirmed that Fabregas has a hamstring injury, while Ramires is suffering from a groin strain.
Mourinho said: “Every player was fantastic and some were absolutely brilliant but Ramires and Fabregas both played injured.
Fabregas is a fantastic professional and he gambled and I gambled
“Maybe the team will lose them for a match or two now but they put themselves there for the team, like I am sure others will in the future because the spirit of the team is fantastic.
“Fabregas has a hamstring injury, Ramires is the same thing [groin] as before but he knew for my plan it was important for him to start the game.
“Fabregas is a fantastic professional and he gambled and I gambled. He can join up with Spain but if he does he will be back.”
Mourinho is also grateful to the Spanish FA for allowing Diego Costa to remain at Chelsea and work on his fitness during the forthcoming international break.
Asked about Costa, Mourinho replied: “He is back. Maybe the injury was good because it made him stop, and when he has to stop he had time to recover step by step.
“In this moment he is in good condition and Spain made a fantastic decision for them and for us.
“Now he has 15 days to be at the top of his game and when Spain needs him they will have a good Diego, not a bad Diego.”
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