The 34-year-old was forced to withdraw due to a detailed pre-planned training and medical programme he has been told to follow to help manage a long-standing back problem.
England boss Roy Hodgson met Ferdinand on Sunday before taking the decision to replace him with Tottenham's Steven Caulker.
At the meeting, Ferdinand confirmed he was keen to continue his England career and hoped to be selected for the summer and autumn fixtures ahead of the 2014 World Cup finals in Brazil.
It had been thought Hodgson would rest the 81-times capped defender for Friday's trip to San Marino but would consider him for the Montenegro tie four days later with Michael Dawson ruled out through injury.
"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," said Hodgson.
"However, I was pleased he 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 said: "It was important for me to be able to speak with Roy face to face and explain the situation.
"One thing I made clear was my passion and commitment to represent my country is as strong as ever.
"It's disappointing I won't be able to play a part in the upcoming games but I told Roy I want to continue to be available for England and look forward to working with him in the future."
Caulker has been called up from Stuart Pearce's U21s for the senior matches on Friday, March 22 and the following Tuesday.