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By 1966, Ellis was fighting as a heavyweight. When Ali was stripped of the world title for refusing to enter the military, the World Boxing Association staged an eight-man tournament that featured most of the top heavyweight contenders. Ellis, with eight consecutive wins, was invited to be in the tournament.
Joe Frazier, the widely accepted #1 contender, chose not to participate in the tournament. Instead, Frazier fought and knocked out Buster Mathis for the vacant New York State Athletic Commission World Heavyweight Championship.
In his first WBA eliminator, Ellis impressively stopped Leotis Martin in nine rounds on cuts. The fight was about even at the time of the stoppage, but Ellis' sneaky and fast right hand had been a continual danger to Martin throughout. In his next fight, Ellis dropped iron-jawed Oscar Bonavena twice on his way to an easy fifteen-round unanimous decision to reach the WBA tournament final.
On April 27, 1968, Ellis defeated Jerry Quarry by a fifteen-round majority decision to win the vacant WBA World Heavyweight Championship. The referee scored the fight 7-6-2 for Ellis, while the two judges at ringside scored it 10-5 for Ellis and 6-6-3, respectively. Sports Illustrated called Ellis' performance "a tactical masterpiece." Quarry said, "If they'd given me the decision, I'd have given it back. I didn't deserve it.".