CA said Warne was fined for failing to list himself as captain during the Melbourne Stars' semi-final loss against the Perth Scorchers at the WACA last week in an effort to dodge penalty for slow over-rate.
Warne did not appear in the hearing today and was instead represented by Melbourne Stars CEO Clint Cooper and team manager Ben Robertson.
"On 5 December 2012, KFC T20 Big Bash League teams were sent a memo by Cricket Australia," a Cricket Australia statement said.
"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's team-mate James Faulkner was listed on the Melbourne Stars team sheet as captain for the clash against the Scorchers and took part in the coin toss with Perth Scorchers skipper Simon Katich.
CA said Warne was found guilty of breaching Rule 5: Laws of Cricket and Spirit of the Game by Commissioner Arthur Lodge.
Warne had previously been issued with one strike for a slow over-rate violation and a second strike this season would have resulted in an automatic one-match suspension.