The decision was taken following a meeting on Sunday with England boss Roy Hodgson.
"I'm disappointed Rio will not be available, but due to the detailed medical programme he must follow it's not possible," said Hodgson.
Ferdinand later said on Twitter he was "gutted" but said it was necessary as part of his "intricate pre-planned programme".
In a statement he added: "It was important for me to be able to speak with Roy face to face and explain the situation, and one thing I made clear was that my passion and commitment to represent my country is as strong as ever."
And Hodgson said despite Ferdinand's withdrawal and concerns over his fitness he would still be considered for future internationals.
"I was pleased that Rio called and asked to meet with me," Hodgson added. "It was important to hear from him personally about the way he must manage his body between games.
"This is not to say he cannot play back-to-back games - he can and has proven so. He's out this time due to particular pre-planned details already in place for his programme.
"I must place on record how I was impressed with his commitment to playing for England and I look forward to hopefully selecting him for squads in the future."