Mbappe moved joint-fifth in the list of all-time list of Champions League scorers when he netted the opener in a
But both the Frenchman and Brazilian Vinicius Jr were subjected to jeers from the home support at the Bernabeu.
Both players have been criticised for their lack of defensive work but Mourinho says the criticism is because people "want to get a piece" of the duo.
"In Portuguese, we have a proverb that says we only throw stones at the trees that have fruit," Mourinho said when asked about winger Vinicius Jr.
"So what Vini has done here over recent years - how many CL has he won, how many goals has he scored, how many balls has he won? His achievements speak for themselves so he is the tree that has a lot of fruit on it and people want to get a piece of Vini.
"During this digital era where we have access to so many stats, we can tell that he is very close to getting to his best version. He's even set some records already. The stats and numbers he registers suggest we will see his best version very soon. "
Mourinho provided a similar defence of Frenchman Mbappe, who is after scoring 42 goals in 44 games for his club last season.
"I want to remind you of the proverb I said before. He is the tree with a lot of fruit," Mourinho added.
"Obviously a player who scores more than 40 goals for a team is never a problem.
"I saw Kylian giving it his all. He was defending like an animal, even when he had nothing left. His attitude is incredible. It is a joy for me to see a player like that. "
Despite Mbappe's goals, Real Madrid did not win a trophy last year and Spanish football expert Guillem Balague said that could be one of a few reasons why the home fans were booing.
"I don't think anyone really knows [why]," Balague told 5Live's
"There was a bit about the past, of two years of no winning. But the two main stars are not that liked by the fans.
"Mbappe feels a little bit cold, sometimes he can be like Cristiano Ronaldo and he speaks like he is bigger than Real Madrid. And also, he said no to Real Madrid about three times before and maybe they haven't forgotten that - but without Mbappe's goals, the club would be in a very different place.
"And Vinicius worked really hard without the ball, but they just don't forgive him anything even though he did renew his contract. It's a bit of a mystery but I think he is feeling the heat of it. "
