Manchester United manager David Moyes confirmed before Sunday afternoon's 1-0 defeat at Liverpool that Rooney would miss out after suffering a nasty head wound in training on Saturday.
Now it has been confirmed Jones and Johnson will also be unavailable after suffering ankle injuries during the Anfield encounter.
"England have called up Steven Caulker following the withdrawal of three players from Roy Hodgson's squad due to injury," said an FA statement.
Manchester United pair Wayne Rooney and Phil Jones have both left the squad. Glen Johnson, the Liverpool defender, has also withdrawn following his side's win over Manchester United at Anfield."
Cardiff defender Caulker has one England cap to his name, having started and scored against Sweden in Stockholm in November 2012.
There is also a doubt over Liverpool match-winner Daniel Sturridge, who confirmed after the game he had been struggling with a groin injury.
It is the kind of scenario Hodgson feared when concern was expressed over such high-profile matches taking place immediately before an international game.
The good news, such as it was, came from Arsenal boss Arsene Wenger, who confirmed the illness that forced Jack Wilshere off in this afternoon's victory over Tottenham at the Emirates Stadium was nothing serious.
"He has a stomach bug," said Wenger.
"It's nothing that will stop him from going to England."
Nevertheless, Hodgson's plans for the forthcoming double header against Moldova at Wembley on Friday and Ukraine in Kiev four days later are now in turmoil.
The loss of both Jones and Johnson means Tottenham's Kyle Walker, whose only competitive England starts have both come against San Marino, will now almost certainly fill the right-back role for matches that could well go a long way to determining whether the Three Lions qualify automatically for Brazil 2014.
The news will not have improved Hodgson's mood following a quite remarkable snub at Anfield.
Hodgson was unhappy upon his arrival at the stadium to discover he had not been offered the courtesy of a ticket to the directors' lounge, as would be customary for an England manager.
He was then less than impressed to discover his seat for the game was in a row he believed was reserved for scouts rather than in the main area of the directors' box.
Liverpool later claimed this was not the case and Fabio Capello had sat in exactly the same place when he visited Anfield.
However, they acknowledged a ticketing mistake, for which a club official apologised to Hodgson directly at half-time.
Evidently though, this did not appease the Three Lions chief, who spent six unhappy months as Liverpool manager in 2010 before being sacked and replaced by Kenny Dalglish.
Instead of heading to the directors' lounge following the club's intervention, Hodgson opted to sit on his own in the main entrance area at half-time.
He then abandoned his post-match plan of meeting assistant Gary Neville, who had been commentating on the game, to leave five minutes early and head straight to St George's Park.