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Aloisi, who secured Australia's place in the 2006 World Cup after slotting home a winning play-off penalty against Uruguay, said it was in the best interests of the club that he stand down.
"For the past three-and-a-half years, I have given every minute of my life to make the Brisbane Roar a success," he said in a statement.
"Upon reflection of the current situation, I have made the difficult decision to stand down effective immediately as I believe this is in the best interest of the playing group and football club."
The Roar are ninth in the 10-team A-League table with just one win and five losses from nine matches.
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The club said Darren Davies would take over as interim coach until a new one is appointed.