Towards the end of a low-key stalemate at London Stadium that saw United guarantee they will finish in second position, Pogba caught the West Ham captain with a late challenge.
Noble reacted furiously and rushed to confront the France international, appearing to push his hands into his opponent's face.
While both players earned yellow cards from official Jon Moss, Mourinho had a different view of the incident.
"The referee handled the game well," Mourinho said at a post-match news conference.
"I was watching images [of the incident] and Paul and Noble looked in love.
"Hugs and kisses at the end so that was good. It was a competitive game."
Mourinho's counterpart David Moyes also felt the flashpoint required little serious discussion.
"I have got to say I didn't make much of it," Moyes said.
"I saw there was a bit going on but the game had not been that type of game all night, there was a wee bit that came out of nowhere really but I wouldn't make anything of it.
"After 37 games, the players are all getting ready for a break."