Johnson out of England friendly
The 25-year-old played the full 90 minutes at Anfield on Monday before joining up with his international team-mates the following day, where he underwent a routine recovery session while the rest of Fabio Capello's squad trained at Arsenal's London Colney complex.
It was during this session that his knock became apparent and he will now return to his club for treatment, with Capello at this stage not planning to call up another player for the trip to Qatar to face Dunga's team.
It leaves Wes Brown as the only out-and-out right-back remaining, although James Milner or Shaun Wright-Phillips could drop back from midfield.
David Beckham is unavailable due to Major League Soccer commitments in the USA, but Capello's other 22 players from his original squad all trained ahead of the friendly against the South Americans in Doha.
Fitness coach Massimo Neri led the warm-up for the players, then Robert Green, Ben Foster and Joe Hart trained separately with goalkeeper coach Franco Tancredi.
With Portsmouth's David James not in the squad due to fitness, Green could be in line for a return to the starting XI after starting six consecutive matches before his dismissal against Ukraine, which led to Foster starting in the Belarus qualifier.