Australia were on track to claim their first win over the Samurai Blue in Japan after a horror own goal by Shogo Tanaguchi in the 58th minute gave the Socceroos the most unlikely of leads in front of 58,730 fans at Saitama Stadium.
Tanaguchi inexplicably tried to clear a Lewis Miller cross with the outside of his right boot instead of using his left, and sliced the ball past goalkeeper Zion Suzuki.
But 18 minutes later, Burgess knocked a Keito Nakamura squaring ball into his own net, with the Socceroos having to desperately defend to hold on for their first point in Japan since 2013.
Australia have five points from their first four games and currently sit second in group C behind Japan (10 points), pending other results - with the top two teams qualifying directly for the 2026 World Cup.
Australia's Cameron Burgess is consoled by goalkeeper Joe Gauci after conceding his own goal. (AP PHOTO)
The result further magnifies the importance of Australia's huge home clash with Saudi Arabia at Melbourne's AAMI Park on November 14 - which talisman Craig Goodwin will be suspended for after a late booking.
When looking at the bigger picture, a draw is a huge result.
The Socceroos also had to deal with an untimely hiccup, their team bus arriving at the ground only 45 minutes before kick-off at Saitama Stadium on Tuesday night after being caught in traffic due to an accident.
The  Asian Football Confederation knocked back requests from both Football Australia and the Japanese Football Association to delay kick-off.
Popovic turned to 34-year-old debutant Luke Brattan to replace Aiden O'Neill (illness) in midfield, while he also dropped Goodwin to the bench among six changes.
A hard-fought draw away from home 🙌— Subway Socceroos (@Socceroos) #Socceroos #JPNvAUS pic.twitter.com/mizUgWdDpCOctober 15, 2024
But Brattan - the oldest Socceroos debutant since 1963 - struggled and was hooked for Patrick Yazbek at half-time
Japan had a golden early opportunity to score in the sixth minute when Takefusa Kubo found himself in space but shot into the side netting.
A minute later, Mitch Duke turned a header way off target - a rare Australian chance.
Australia rarely threatened but only allowed Japan one shot on target from six attempts in the first half.
In the 57th minute, Kubo brilliantly picked out Takumi Minamino at the back post but the attacker headed wide.
A minute later, Tanaguchi gave away his own goal to hand Australia a welcome lead, but their delight was relatively short-lived.
After Burgess' own goal, Japan sent in wave after wave of attacks but Harry Souttar and Gauci stood tall late to save the point.