Usyk produced a commanding display in front of 90,000 fans inside Wembley Stadium, dropping Dubois twice in the fifth round.
The second knockdown proved decisive, with a trademark left hook that left the Brit unable to beat the count.
At 38, Usyk, 11 years older and more than a stone lighter than his opponent, once again proved ageless, extending his perfect professional record to 24 wins.
"38 is a young guy, remember," he later declared in the ring, dropping to his knees in celebration.
Victory saw Usyk reclaim the IBF title, stripped from him last year despite unifying the division, and add it to the WBA, WBC and WBO belts he already held.
It marked his second stoppage win over Dubois, having previously beaten him in 2023.
For Dubois, the loss halts a promising resurgence after his stunning win over Anthony Joshua in September. He now falls to 22-3, with all three defeats coming inside the distance.
“I gave everything I had,” he said after the fight. “Take no credit away from that man (Usyk). I’ll be back.”
Usyk, who unified the cruiserweight division before moving up, further cements his legacy as one of boxing’s modern greats.
Asked about his next opponent, he told DAZN: "Maybe it's Tyson Fury. Maybe we have three choices... Derek Chisora and Anthony Joshua. Maybe Joseph Parker."