And manager Roy Hodgson has therefore decided to add Cardiff defender Steven Caulker to his squad for the crucial fixtures.
Key forward Rooney had to miss Manchester United's 1-0 loss to Liverpool on Sunday after sustaining a nasty head wound in training on Friday.
United manager David Moyes said: "He got a cut down the middle of his forehead. It was completely accidental but it was quite a bad cut.
"It will probably keep him out for around three weeks."
England's regular right-back Johnson and the versatile Jones, who can play in defence or midfield, then picked up ankle injuries during Sunday's Anfield encounter.
Sturridge battling a groin injury
There is also a doubt over Liverpool's Daniel Sturridge, who scored the winner against United but confirmed afterwards that he was struggling with a groin injury.
However, Jack Wilshere, who had to go off before half-time during Arsenal's 1-0 win over Spurs, is not a doubt for the England matches.
"He has a stomach bug," said his club manager Arsene Wenger. "It's nothing that will stop him from going to England."
The England squad are to meet at St George's Park on Monday and Caulker, who has one previous cap to his name, has been called up following the injuries.
The 21-year-old former Spurs man started and scored in the friendly in Sweden in November last year and England were 2-1 up when he was substituted, although they went on to lose 4-2.
England are at home to Moldova on Friday night and then face a critical qualifier in the Ukraine the following Tuesday.
Hodgson's men are currently second in qualifying Group H, two points behind Montenegro and one ahead of Ukraine.