Fury, unbeaten holder of one of the sport's most prestigious belts, narrowly avoided a first defeat at the hands of an opponent who had never boxed professionally before but went through the full 10 rounds with some swagger.
Ngannou dropped the Briton to the canvas in round three with a left hook and although the self-styled "Gypsy King" was able to see out the round he had no doubts about what he was up against.
"That definitely wasn’t in the script," said Fury after two of the judges gave him the win 96-93 and 95-94. The third judge scored it 95-94 in favour of his Cameroon-French opponent.
"He’s a hell of a fighter and a hell of a lot better boxer than we thought he would be. He’s an awkward man and a good puncher and I respect him a lot.
"He’s given me one of my toughest fights of the last 10 years."
Fury said there was no rematch clause but he would like to fight Ngannou again "down the line", after an undisputed title fight with Ukraine's IBF, IBO, WBO and WBA champion Oleksandr Usyk.
The pair are set to meet in Riyadh at a date yet to be announced officially but that both champions said will be December 23.
Usyk, who was in Saudi Arabia to watch his future opponent, said he was ready.
Ngannou vacated his heavyweight belt after a contract dispute with UFC and exited as a free agent in January.
"My training camp was only three and a half months and I came into this with an injury. But I don’t want to give excuses. I will look at what I can do next to improve my game to come back even better," he said.
"Now I know I can do this... get ready. The wolf is in the house."
