Benfica meet Newcastle in the Champions League tonight, with Mourinho impressed by how the Toon sold Isak and replaced him with Nick Woltemade.
Mourinho said: "What happened with Isak in the summer is very difficult for a club and very difficult for a coach and very difficult for the fellow players.
"I think in the end everybody knows he is going to leave to Liverpool. But one thing is everybody knows he is going to leave, and another is it is done.
"When it is done you can move on, when it is done you can have a new player and when you have a new player you can start to train and adapt to play with the new player because of course Isak and Nick Woltemade are different players."
Woltemade goes into the game on the back of another goal against Brighton to take his tally for all teams to seven goals for the season. Mourinho, who wooed the Tyneside media during a captivating 30 minutes Press conference, said: "There is always a transition but it looks like this boy (Woltemade) has been playing here all his life.
"Because he is performing, adapting and loved by the fans. Newcastle are doing things right, doing things right."