A double from substitute Papiss Cisse put the hosts ahead and, despite the Magpies being reduced to 10 men and Didier Drogba scoring with time to spare, the Blues were unable to find a late equaliser to cling into their record.
And the Portuguese boss was furious with the home side's ball boys and their delaying tactics, even suggesting that the match officials should have awarded more than the six minutes of stoppage time that was added on.
"We wanted to play more football, but that was not possible because a few things that I thought didn't belong any more to top level football but still belongs - the ball disappears, the ball doesn't come, another ball comes, the ball boys they run away," Mourinho told BT Sport.
"These are the kinds of situation which our unfortunately still part of the game. But no complaints."
When probed further, he added: "You didn't see that? The ball disappeared. They keep the ball, they hide the ball, we want to play, no ball. When one ball comes the second ball appears again. This kind of strategy."
"I think [more time should have been added on], I think but it's not just about the time because even during the extra time they kept doing the same thing.
"It's also very difficult for the referee to cope with it because [it is] not the players inside the pitch who are doing that so the referee cannot punish any player because the players are just there.
"That is a kind of strategy that is unfortunately still part of the game, but OK, forgetting that, we were very unlucky, we didn't deserve this result but it is the result we have, we have to accept, we have to move on."
The loss ends Chelsea's hopes of emulating Arsene Wenger's Arsenal 'Invicibles', but they remain top of the league, ahead of second-placed Manchester City.