Tommy Oar's fortuitous late strike had looked set to condemn the hosts to an undeserved defeat. But after Matthew McKay handled in the box, Honda drove his spot-kick straight down the middle to earn the necessary point.
The result left the Asian champions seven points clear and uncatchable in Group B, putting them through to their fifth straight World Cup. It is the first time they have sealed qualification on home soil.
Japan coach Alberto Zaccheroni, who joined Japan after the 2010 World Cup, said his attractive Blue Samurai side would "surprise the world" at next year's tournament in Brazil.
"I came to Japan to bring them to the World Cup -- that was my bottom line," said the Italian. "I feel relieved that I achieved it. We are going to improve further and surprise the world."
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Holger Osieck's Australia meanwhile will be glad of the point away from home as they scrap with Jordan, Oman and Iraq for the second automatic qualifying spot. The third-placed team will go into a play-off.
Yasuhito Endo's dipping free-kick curled past the upright early on, and the Gamba Osaka midfielder then fired over the bar after a slick move orchestrated by Honda and Manchester United's Shinji Kagawa.