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The match had been in doubt after FIFA announced on Monday it was suspending the reigning Asian champion in response to its government's decision to dissolve its National Olympic Committee.
However, FIFA agreed to revoke the ban after the Iraqi government provided written assurances that it had not dissolved the Iraqi Football Association.
The lifting of the ban has Australia worried.
Pim Verbeek, the Dutch coach of Australia, was happy the match would be played but warned his players Iraq will go in as more dangerous opponents now they have won their fight to play.
"This is definitely not to our advantage what has happened," Verbeek said.
"They will want to show everybody they deserve to be in the World Cup and we have to be alert on that.
"It was not going to be an easy game already and it will be more difficult now."
Australia, which leads Group 1 with four points from two games, would have received six points for two forfeited games, including the return leg on June 7, had the ban been put in place, and one foot in the next qualifying round.
However the green light for the game prevented a heavy financial cost for the scrapping of a home fixture before a sell-out crowd, and provided a chance for the predominantly European-based squad to play a competitive game in its club off-season.
Asian champion Iraq is bottom of Group 1, which includes Qatar and China which meets on Monday, with one point from two games. The top two teams from each group will proceed to the final qualifying round.