The 25-year-old Manchester United defender suffered an injury in Friday's international friendly that Mourinho says will sideline him for the Premier League game against Newcastle.
Jones had been struggling with a thigh problem before the international break but joined an injury-hit England squad.
Tottenham trio Harry Kane, Harry Winks and Dele Alli, Manchester City duo Raheem Sterling and Fabian Delph and Chelsea midfielder Danny Drinkwater were among those who were unavailable for England's friendlies with Germany and Brazil.
Mourinho admitted he may have been naive in comparison to the managers of his Premier League title rivals by allowing his player join up with Gareth Southgate's squad, but believes Jones should not have been risked.
"I don't think it is possible for a player with a problem to play in a friendly," the United manager 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 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 mangers are naive, too pure and they say you have to go and they go and sometimes 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. Drinkwater? Delph? The only one that is not playing is Phil Jones."
Mourinho also confirmed forward Zlatan Ibrahimovic is expected to return to the United team before the end of the year from the knee injury he suffered in April.
He told Sky Sports: "He is a lion, he is a fighter. I think that is a good description of him, he has the anger all the time and that's the reason why he's almost coming back.
"As we expect, he's reduced the timing of his recovering and he will be back in 2017, which is a magnificent recovery."