The two have enjoyed a frosty relationship during their time together at Old Trafford with both seemingly critical of the other for much of this season.
The situation came to a head last month when the pair were pictured sharing what appeared to be a particularly icy exchange during training.
But Pereira, who was part of the Instagram video in question taken during the EFL Cup game with Derby, has revealed what really happened.
"It was in a cup game," he told UOL. "Pogba posted the video before and there was me and left-back Luke Shaw laughing.
"We were winning the game 1-0 at the time of the video. Then we lost the game, and people said that Pogba posted later. But he posted before.
"The manager thought that Pogba had posted later. He asked him why did that happen. There was a mood about it. These things were out here in England. But it's like, I have nothing to do with it.
"Mourinho gave me a chance, he said to me: 'I want you to stay here'. It would be a shot on my own foot to badmouth the guy who gave me the first opportunity to play and is still giving it."
Mourinho's future at the club remains firmly in doubt after a disappointing season up to now.
The last-gasp win over Newcastle appeared to hand the Portuguese a stay of execution and Pereira says the dressing room remain behind the manager.
"The relationship is good, it's cool," he added. "I have a very good relationship with him, with the players. And he also has a good relationship with the players.
"We don't feel that pressure coming from outside. Everyone says that he's being sacked. We do not feel that.
"For you to have an idea, I don't usually have any English media on my phone so I don't get intoxicated with everything they say.
"He's our manager, we give our life on the pitch for him and for us too. Everyone is very calm, very focused and very happy."