Jones will miss Wednesday's Champions League clash at Basel and the visit of Brighton and Hove Albion in the Premier League on Saturday, Mourinho said.
England's next matches are against Netherlands on March 23 and Italy four days later.
"I hope (Smalling) doesn't get his spot (in the England team) because somebody comes (back) injured, he comes injured, Jones comes injured and real injuries," Mourinho told reporters.
"Our injuries are real injuries. Jones does not play tomorrow and I can say in advance he doesn't play the weekend too.
"Smalling is playing all the time and... tomorrow plays again. We don't have Jones, we don't have Eric Bailly again, so Smalling has to play every match and well."
Centre back Bailly could be fit for the weekend, while striker Zlatan Ibrahimovic, who returned from a long-term knee ligament injury last weekend against Newcastle United, will start on the bench in Switzerland.
Mourinho said United's doctors had not been informed about Jones receiving pain-killing injections before facing Germany at Wembley, the game in which he was injured, but ruled out taking the lack of communication up with England boss Gareth Southgate.
"I'm not a doctor," he said. "(The England doctors) consult my doctor in relation to Jones with a little problem in the knee when the national team starts working and then no more contact.
"And then the local injections before the match, we were not informed. Apart from that I don't have to speak with Southgate."
Mourinho said his comments about Smalling were from a selfish perspective and added that in reality he wanted his players to be happy and play for their national teams.
"I say in a selfish perspective but it is not a real perspective because what I want is my players to be happy and go to the national teams and an event like the World Cup," he said.
United top Champions League Group A with 12 points from four matches, while Basel are second on six points, ahead of CSKA Moscow on goal difference.
(Reporting by Toby Davis)
