The 65-year-old, who most recently coached Saudi Arabia, replaces Ange Postecoglou, who stood down after taking the Socceroos through two playoffs to qualify for Russia.
"This is a great result for Australian football, Bert Van Marwijk is world class," FFA chief Stephen Lowy said in a statement.
"He took the Netherlands to the World Cup final in 2010, he led the Saudi Arabian team to qualify directly for this year’s Finals and most importantly, he knows a lot about our team and how they play because he studied them closely as an opposition manager in the same group.
"These experiences make him a compelling choice."
Australia will play France, Denmark and Peru in the pool stage at the June 14 to July 15 finals, their fourth successive appearance at the World Cup.
For full coverage, including FFA CEO David Gallop's thoughts on the new coach, visit The World Game.