Already trailing after Christian Eriksen struck 11 seconds in at Wembley on Wednesday, United's task got more difficult when Jones turned a Kieran Trippier cross into his own net.
Speaking after the 2-0 defeat that left his team 15 points adrift of leaders Manchester City, Mourinho said it was the type of goal the Premier League's top goalscorer Kane would be proud of.
"We made a bad mistake in the first goal, a mistake by the whole team, they watch videos and they analyse the Spurs kick-off," he told BT Sport.
"We lose the first ball, the second ball on the ground and the cover inside for Eriksen, so a really, really, really bad goal.
"It was a good reaction for 10 minutes but then the second goal mentally killed us and gave Tottenham the possibility to play the way they like to play.
"Jones had a bad contact with the ball and scored an amazing goal Harry Kane would love to score."
Making matters worse for United, midfielder Marouane Fellaini was substituted just seven minutes after coming on in the second half.
Mourinho confirmed the Belgium international had again injured his knee, although he is unlikely to be sidelined for a prolonged period.
"I was unlucky with Fellaini. I wanted to change the structure and after a couple of minutes he was injured," he said.
"It's always the same thing, the lateral ligament. I don't think it's a big thing but he was telling us he couldn't carry on."