Group B leaders Japan went ahead in the 65th minute when Yuzo Kurihara netted from close range, after Keisuke Honda jinked his way along the byline, five minutes after the hosts had substitute Mark Milligan sent off for a questionable second yellow card.
But Australia won a penalty when Atsuto Uchida was penalised for holding striker Alex Brosque at a corner and Wilkshire converted by blasting his spot-kick down the middle.
Japan were also reduced to 10 men late on with Kurihara picking up a second booking in the 89th minute.
The draw keeps Japan top of the five-team pool with seven points from three games, while Australia are second with two from two.
Korea Republic made it two wins from two at the top of Group A with a 3-0 home win over Lebanon in Goyang.
Kim Bo-kyung scored in the 30th and 48th minutes to put the hosts in control before Koo Ja-cheol rounded off a comprehensive victory in the 90th minute.
Lebanon are bottom of the pool with one point from three games.
Iran and Qatar are level on points in second and third respectively behind Korea Republic following a goalless draw in Tehran on Tuesday.
In Group B, Iraq moved level on points with Australia as they drew 1-1 with Oman in Doha.
Oman took an eighth-minute lead when Mohammed Al Balushi headed in a free-kick, but Younis Mahmood levelled from the penalty spot eight minutes before half-time after Abdul Al Mukhaini handled in the area.
Tuesday's AFC 2014 World Cup Qualifying Results
Korea Republic 3-0 Lebanon
Iran 0-0 Qatar
Australia 1-1 Japan
Iraq 1-1 Oman