Blatter had asked to be kept informed about the Bolton midfielder following his collapse at Tottenham last Saturday and was informed by club chairman Phil Gartside when Muamba regained consciousness.
The 23-year-old is still in intensive care but has been able to speak to family and friends.
Blatter, a deeply religious man who accompanied the body of Marc-Vivien Foe back to Cameroon after his death during a Confederations Cup match in France in 2003, said in an interview in Istanbul: "It's a miracle. When I saw it on the television, it was terrible.
"I had a phonecall from Phil Gartside, the chairman of Bolton, and I have to say it was a very emotional call and, as he said, from time to time there are forces somewhere, that have nothing to do with reality. He spoke about the players who stood all around this guy.
"He was very emotional, and I was emotional as well because I told him the story of how I brought back Foe to Cameroon, how I accompanied him until his funeral.
"His president [Gartside] speaks about the miracle and I speak about a miracle as well. I am a deeply faithful man, a religious man, and I believe there is something more than just playing the game. There is somebody who looks after us."
After Foe's death, Blatter was instrumental in urging clubs and national associations to regularly carry out cardiac screenings for players, especially young players.
Blatter added: "This player had heart screening last year and it should be done for everyone, in repetition but especially for those in competition in football or other sports."
Dr Sam Mohiddin, the consultant cardiologist treating Muamba at the London Chest Hospital, said the player has continued "to demonstrate positive signs of recovery" and had "exceeded our expectations and our hopes".