Jones lasted less than half an hour of England's goalless draw with world champions Germany on Friday before limping off with a thigh problem which he has been struggling with in recent weeks.
Mourinho confirmed that Jones will miss Saturday's Premier League clash with Newcastle United as a result of the injury and suggested that he was "naive" not to pull the defender out of the squad having seen a host of other players withdraw.
"I don't think it is possible for a player with a problem to play in a friendly. Of course, Phil Jones had a problem," Mourinho told The Mirror.
"He was having a problem for three weeks, he's having problems that are stopping him to play for his club and then he plays for his club in extreme conditions [in their final match before the internationals] because it's a big match against Chelsea. And then he goes to the national team and he comes home with an ongoing injury that everyone knows is an ongoing injury.
"You have always some clubs where their players, they have always have something. It could be a fingernail, he has a little flu, he has a problem with the little toe, and they withdraw, and they stay with their clubs and they have their holidays and they have their rest.
"Then, there are always the clubs where the managers are naive, too pure and they say you have to go and they go and sometimes they pay the price and they pay the price. I want to see this next weekend if the players that were not going to the national team, I want to see if they are going to play. [Danny] Drinkwater? [Fabian] Delph? The only one that is not playing is Phil Jones."