The Melbourne Renegades player has a suspected fracture of the eye socket suffered on Sunday when he top-edged a bouncer from Melbourne Stars' Lasith Malinga into his face.
He will be replaced by Englishman Alex Hales, Big Bash organisers said.
The Renegades beat Warne's Melbourne Stars to guarantee a home semi-final but the match will be remembered for the heated argument between the former Australian spinner and Samuels.
Warne was banned for one game and fined A$4,500 after being found guilty of three offences, including showing dissent to the umpire, engaging in physical contact with other players and using offensive language.
Samuels, who threw his bat in the direction of Warne after the Stars' captain hit him with the ball when throwing it to the wicketkeeper, was charged with two offences with his case yet to be heard because of his injury.
