The Manchester United defender met up with Roy Hodgson on Sunday evening and took the decision in conjunction with the national boss.
Ferdinand's bespoke training schedule means he is unable to take part in the two games but the defender has said he wants to be considered in the future as England's campaign to reach the 2014 World Cup in Brazil continues.
Tottenham's Steven Caulker has been called up from the Under-21 squad to replace Ferdinand.
Hodgson said: "I'm disappointed Rio will not be available, but due to the detailed pre-planned training and medical programme he must follow it's not possible.
"However, I was pleased that Rio called and asked to meet with me. 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."
Ferdinand was expected to make his first appearance since a 2-2 draw with Switzerland in June 2011 having missed out of the Euro 2012 finals due to Hodgson's infamous "football reasons".
Ferdinand said: "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.
"It is disappointing that I won't be able to play a part in the upcoming games but I told Roy that I want to continue to be available for England and I look forward to working with him in the future."