Hodgson named Ferdinand in his squad for the first time for the Group H qualifiers against San Marino and Montenegro, but said when he announced his squad on Thursday he had not spoken to the player first.
If he had done so, he might have avoided a potentially embarrassing situation following the 34-year-old's withdrawal.
Hodgson had left the Manchester United centre back out of his Euro 2012 squad for "footballing reasons" amid media speculation it was connected to the John Terry saga.
In a statement on its website, the English FA said the decision to withdraw Ferdinand was taken following a meeting between the player and Hodgson in London on Sunday.
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.
"I was impressed with his commitment to playing for England and I look forward to hopefully selecting him for squads in the future."
Hodgson had said Ferdinand, who made the last of his 81 appearances for England in a friendly against Switzerland in June 2011, was now the best man for the job following a series of excellent performances for United over the last few weeks.
Ferdinand made clear the withdrawal was not a snub.
"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," he said.
"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."
Later he tweeted: "I'm gutted I had to pull out of England squad, but it was the right decision for my intricate pre-planned programme."
Steven Caulker, who was originally named in Stuart Pearce's Under-21 squad, will now join the seniors.
Speculation was rife that Ferdinand was left out of Hodgson's squad for the European Championship after his one-time England central defensive partner John Terry of Chelsea was accused of racially abusing Ferdinand's brother Anton while Anton was at Queens Park Rangers.
Despite Terry now having retired from internationals, meaning Ferdinand would not have to play alongside him, media reports this month suggested he may not accept Hodgson's call-up.
That idea lost credence when his United manager Sir Alex Ferguson said after the match against Reading on Saturday that the veteran would be joining up with the squad, only for it not to transpire.
Ferdinand became the third member of the original squad to withdraw following the news from White Hart Lane on Sunday that Tottenham Hotspur pair Michael Dawson and Aaron Lennon were both injured and would not be available.
As well as Caulker being added to the squad, Manchester City defender Joleon Lescott has also been called up for the games in San Marino on Friday and Montenegro next Tuesday.
Montenegro lead the group on 10 points from four games with England second on eight.
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