Ngannou, 37, put Fury on the canvas in round three after connecting with a left hook.
But while one judge scored it 95-94 in favour of Ngannou, two gave it to Fury at 96-93 and 95-94.
Fury’s WBC heavyweight belt was not on the line.
“That definitely wasn’t in the script,” Fury told TNT Sports.
“I got caught round the back of the head [for the knockdown]. I wasn’t hurt. I got up and got back to my boxing.
“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’s victory means a blockbuster bout with fellow heavyweight champion Oleksandr Usyk – who holds the WBA, WBO and IBF titles – which was agreed earlier this month, remains on the horizon.
An undisputed heavyweight contest, the first in the four-belt era, has been mooted for 23 December, but a cut and bruised Fury might struggle to recover so quickly.