Muralitharan ruled himself out of the series following the controversy about his action.
Australia fell two wickets short of victory in Cairns with Sri Lanka hanging on for the draw at 183 for eight having been set 355 to win.
Matthew Hayden hit 132 - his second hundred of the match - to guide the hosts to 292 for nine declared.
He passed 5,000 runs on the way to his 20th century in Tests and was named man of the match and the series.
Fast bowler Glenn McGrath was fined 25 percent of his match fee for an audible obscenity after a leg before appeal against Sanatha Jayasuriya was turned down.
