The Manchester United captain also missed Tuesday’s session along with Liverpool’s Danny Ings and Swansea City’s Jonjo Shelvey.
Rooney picked up an ankle injury in Man United’s 3-0 defeat against Arsenal last weekend.
England have already qualified for the European Championships next summer and Rooney may be used in the game against Lithuania next week instead.
England training at SGP. No Rooney, Ings or Shelvey pic.twitter.com/URjWD8TKrY
— Paul Hirst (@hirstclass) October 7, 2015
Even if Rooney does not make the Estonia clash, he will be presented with a golden boot by Sir Bobby Charlton to mark breaking the England goalscoring record.
Rooney has been going through a tough time at United and there have been numerous calls from supporters for him to be dropped from the starting XI. Perhaps sitting out England’s game against Estonia, and possibly the one with Lithuania, will give Rooney some rest and time out of the limelight before he returns to United.