Goals from Demba Ba, after a costly slip from Steven Gerrard, and Willian saw the Blues claim all three points at Anfield but their manager isn't convinced they can finish top.
Goals from Demba Ba, who capitalized on an uncharacteristic error from Reds skipper Steven Gerrard, and Willian secured all three points for Mourinho's men in a game that was being billed as a title showdown.
The result sees the Blues close the gap on the Merseysiders to just two points, with both sides having two games left to play in the 2013-14 Premier League campaign, although Mourinho does not believe his team are now back in the running.
When asked if his team is in the title race, he told Sky Sports: "No, we're back in nothing. In this moment we are almost third. Yesterday with Everton in fifth we were automatically qualified for the Champions League but fourth was still a possibility.
"Now with these three points we need one point to finish third. It was a good season for us. There was an evolution in many aspects of this team. And now champions are only one and the champions will be City or Liverpool. So we have nothing to celebrate but we can say that we finished third and we can say we won both matches against the champion."
Chelsea defended resolutely and repelled waves of Liverpool attacks over the 90 minutes and Mourinho was full of praise for side, singling out Tomas Kalas, who was making his Premier League debut, for his performance.
"My feeling is that we deserved to win, no doubts about it. It's as simple as this," he said. "And with the result 1-0 during the first 45 minutes, we were always comfortable and we were never in trouble against a fantastic team
"For us to have this performance and for a kid like Kalas to make his debut and play the way he did - all of them, I have to speak about the kid because it's a special day for him, our team was fantastic and a very much deserved victory. We won both matches against the champions - whether it's Liverpool or Man City."