Mourinho hooked Pogba with ten minutes left to play after the Frenchman had put in an impressive performance.
The United boss opened fire on Pogba after the 1-0 defeat to West Brom last weekend, but Mourinho will have been pleased with the reaction from his player.
But there was no handshake for Pogba when he trotted off the pitch and Mourinho only shot a glance and a thumbs up in the direction of his star Red Devil.
Pogba shook the hand of the two coaches sitting beside Mourinho, but did not offer the same to his manager. The playmaker then went straight down the tunnel, before returning to the bench.
The exchange will only add to speculation that Pogbas and Mourinhos relationship is at an all-time low.
Mourinho has repeatedly hit out at his star this season and has dropped the £89million man from his starting eleven on numerous occasions.
Pogba will be hoping his showing against Bournemouth in the 2-0 win will be enough to secure a spot in the side that will take on Tottenham this weekend.
United face Spurs in the semi-final of the FA Cup, and Mourinho had warned Pogba and others that they were not guaranteed a place in the team.
More: Manchester United FC