An explosive ninth round in which Fury was given a 10 count after reeling from a series of left hands before then being saved by the bell swung the contest in the new WBC, WBA, IBF and WBO champion's favour.
Usyk won 115-112 and 114-113 on two scorecards while the third judge saw it 114-113 for Fury, who felt he should have been given the decision.
Usyk has missed children's birthdays and even the birth of his daughter during his eight-month camp for the Fury fight, originally scheduled for February before the Briton suffered a cut in training.
His promoter Alex Krassyuk believed that Usyk was denied a knock-out victory when the referee stepped in as Fury looked about to hit the deck in round nine.
"I believe the referee saved Tyson from a knock-out and stole the ninth-round knock-out, which should have happened," Krassyuk said.
Usyk was taken to hospital for a scan on an injury that his promoter Alex Krassyuk refused to disclose after inflicting the first loss of Fury's career in an enthralling clash that surpassed expectations.
An explosive ninth round in which Fury was given a 10 count after reeling from a series of left hands before then being saved by the bell swung the contest in the new WBC, WBA, IBF and WBO champion's favour.
Tyson Fury appeared to claim that he lost his showdown with Oleksandr Usyk because the judges sided with the Ukrainian over the war in Ukraine.
"I believe I won that fight," Fury said. "I believe he won a few of the rounds, but I won the majority of them, and I believe it was one of those what-can-you-do, one of them ... decisions in boxing. We both put on a good fight, best we can do.
"You know, his country is at war, so people are siding with a country at war."
Usyk said he wanted to focus on his family, rather than boxing, and he shed tears at the press conference as he remembered his late father who died just days after he won the Olympic heavyweight title at London 2012.
Tyson Fury is a dad-of-seven, has £300m in bank and has earned the right to surrender – so why didn’t he against Usyk, writes Sun boxing reporter Wally Downes Jr.
Read Wally's big fight verdict in the link, below.
How the big fight went down last night as Oleksandr Usyk became the undisputed heavyweight champion of the world with his stunning win over Tyson Fury:
Here is what we know about when the HUGE rematch will take place.
Saudi boxing chief, H.E. Turki Alalshikh, confirmed before the fight started that Fury vs Usyk II has been pencilled in for the weekend of October 12/13.
Alalshikh plans to have the rematch to kick off another Riyadh Season.
Matchroom Boxing chief and Anthony Joshua promoter Eddie Hearn has given his thoughts on Tyson Fury's stunning survival of the ninth round against Oleksandr Usyk.
He told DAZN: "How he survived the ninth [round]?
"I thought he was very lucky that the referee didn't jump in.
He showed unbelievable heart to stay on his feet and unbelievable composure coming out for the tenth and eleventh rounds.
"He was losing those rounds, but he was recovering."
Oleksandr Usyk faces only being able to call himself undisputed champion for a matter of weeks.
Usyk prevailed in what was been dubbed "the fight of the century" after beating Fury via split-decision in Saudi Arabia.
Fury lost his WBC title, while Usyk added to his WBA, IBF and WBO belts.
And despite all the attention and build up to the first undisputed heavyweight bout in over 25 years, his status will only last a fraction of that time.
Boxing journalist Dan Rafael has reported that the winner of tonight's bout will maintain the undisputed title for "less than two weeks".
It's said that both Fury and Usyk's contracts dictate that they must vacate the IBF title ahead of overdue mandatory challenger Filip Hrgovic's bout with Daniel Dubois.
Lennox Lewis - the last man to hold all the heavyweight titles - took to Twitter to congratulate Oleksandr Usyk for following in his footsteps and becoming the undisputed ruler of the division.
He tweeted: "Welcome to the club! z@Usykaa.
"Tonight we witnessed a crackin’ fight and history made.
"I was happy to welcome either one of these incredible champions to the Undisputed HW club and tonight it was Oleksandr The Great.
"Looking forward to seeing them do it again. @usykaa has proved that it never too late to add to your legacy. Congrats!
"Fury will learn from this and he’ll be back! Losing is also part of the game, it’s how u respond to a loss that makes all the difference."