After an uninspiring first half, Yoan Gouffran gave the Magpies the lead in the 68th minute when he headed home Yohan Cabaye’s free-kick.
And Loic Remy put the game beyond doubt when he stroked in Vurnon Anita cut-back one minute from time to end Chelsea’s three-game winning streak in the league.
“I didn’t like our performance and I think we deserved to lose – it’s as simple as that,” Mourinho told BT Sport.
“We had a good reaction and a couple of good chances to equalise but I think they were more in the game than us.
“They fought more than us and were much more committed than us. For sure they were the best team on the pitch. If somebody had to win, it was Newcastle, not us.
“We were not sharp and not intense with the ball. We defended quite well but we were not fast and intense and aggressive with the ball so we let the game go, waiting for a chance to score a goal.”
The result leaves Chelsea in third place in the Premier League table, with Arsenal able to move five points clear of the Blues should they beat Newcastle later on Saturday.
But Mourinho insists it is too early to read anything into the standings.
“The race is there for everybody,” he continued. “If Arsenal win today and they open the gap, they just open the gap, there’s nothing definite. #
“But I didn’t like my team today. I’m disappointed.”
MORE: Man United latest news
MORE: Arsenal latest news
MORE: Chelsea latest news
MORE: Liverpool latest news