In a statement, CA said Warne is alleged to have breached Rule 5: Laws of Cricket and Spirit of the Game.
Warne, the Melbourne Stars skipper, was not listed on the team sheet as captain and James Faulkner took his place and went out for toss with Perth Scorchers captain Simon Katich for the semifinal match last night.
On December 5, Big Bash League teams were sent a Memo by Cricket Australia. Under the heading 'Over Rates', the Memo stated that "If a team's official captain is selected but not named as captain, this will be considered against the Spirit of Cricket and may attract a Code of Behaviour charge."
Warne had previously been issued with one strike for a slow over rate violation, with a second strike this season resulting in an automatic one-match suspension.
The time and date of this latest hearing is yet to be determined.
Early this month, Warne was banned for one game following a fiery clash with Melbourne Renegades batsman Marlon Samuels in a Big Bash match.
