Australia produced an extraordinary defensive effort to nearly pinch the win - led by goalkeeper Mark Schwarzer, skipper Lucas Neill and his veteran partner-in-crime Sasa Ognenovski.
They soaked up every bit of pressure thrown at them, especially in Japan's high-octane first 20 minutes of the second half in which the dangerous Honda missed a point-blank chance and Shinji Kagawa brushed the crossbar.
European-based stars Kagawa and Honda menaced, manipulated and magicked around the edge of the box all night.
But they couldn't find a way past a Socceroos defence which produced one of its finest performances in years, until McKay conceded a gutting late penalty.
Schwarzer was particularly brilliant, with an amazing one-handed save to deny Kagawa on 19 minutes after his interplay with Shinji Okazaki and Honda neatly unzipped the Australian defence.
Then he spread himself at full stretch in the 80th minute with Yuto Nagatomo bearing down on goal.
Two minutes later, Australia had taken the lead as Oar's floated shot drifted over Japanese keeper Eiji Kawashima for an advantage few saw coming, until Japan levelled through Honda's spot-kick.
Australia's brave result will at least ease the pressure on under-siege coach Holger Osieck after the team's sputtering form in the campaign previously.
As Japan celebrated wildly post-match following their qualification, Osieck admitted there was much disappointment in the Australian dressing-room following the draw, despite the result actually being a positive one in the context of the World Cup campaign.
But he declared himself pleased with the Socceroos' defensive discipline and how they stuck to the game-plan.
"When you are very close to winning such a very difficult game, then of course you are disappointed,'' Osieck said.
"But I told my players they should have their heads up, not question themselves and I think we should gain a lot of confidence from this game to get ready for the two home games in Australia now.''
Neill was thrilled with his side's defensive effort, though gutted to miss out on three points which would have gone a long way to ensuring their participation in Brazil.
"It feels like two points dropped, but I don't think too many people gave us a chance before the game. I did,'' Neill said.
"We possibly deserved three points and it would have set us up lovely. But we'll take the point, and we know we've got two games, and importantly destiny's still in our hands.''
- AAP
