Both teams finished with 10 men and Australia will be more pleased with the result after surviving with a man short for more than half an hour.
Mark Milligan drew a second yellow card in the 56th minute and Yuzo Kurihara capitalised with a goal eight minutes later. But referee Khalil Al Ghamdi stunned Japan by awarding a spot-kick to Australia for an infringement in the 69th minute.
Defender Wilkshire slotted the kick past goalkeeper Eiji Kawashima for the equaliser.
Australia came close to stealing victory in injury time when Wilkshire rocketed a free-kick past the Japanese wall and Kawashima made a great save.
Japan top AFC qualification Group B with seven points from three games while Australia are second with two points from two.
Iraq and Oman, who play later, have a point apiece, as do bottom side Jordan.