Despite hitting the woodwork twice in the first half, the Blues were eventually undone by goals after the interval from Yoan Gouffran and Loic Remy to end a run of five unbeaten matches in the Barclays Premier League.
It was a bad result for a side deemed to be among the title favourites and Mourinho admitted it was a display he wants to forget.
"I didn't like it (the performance) and I think we deserved to lose," the Portuguese told BT Sport.
"We had a couple of good chances to score the equaliser but they were more in the game than us, they fought more than us, were much more committed than us.
"They did much to win and for sure they were the best team on the pitch.
"I told the team (at half-time) that I've been in the game for many, many years and I was smelling what happened because it was quite easy to play the first half.
"We had lots of space but we were not sharp, we were 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.
"I didn't like my team today and I'm disappointed."
Newcastle boss Alan Pardew hopes the three points has shown any doubters his team mean business this season.
He said: "We decided to be very cautious from the start, not let them play for us, and we perhaps let them have a bit too much possession and there wasn't enough pressure on the ball.
"But we knew second half we had enough to exert pressure and the crowd were getting behind us, and that's exactly what happened. The goal came at a great time for us.
"We've got a great spirit in the group. I think we've played well.
"We've had some moments where we've not been so great but we're together. I'm pleased for the club.
"Today was about giving a message to our fans that we're very much alive and kicking. And I'm pleased for everyone associated with Newcastle, it's a big win for us."