The Blue Samurai dominated for most of the match but failed to convert that pressure into goals and Australia winger Tommy Oar looked to have made them pay when his 81st minute cross from the left looped over Japanese goalkeeper Eiji Kawashima, who flapped and failed to clear.
But the Japanese were not to be denied and they poured forward with the equaliser inevitably coming via Honda, who only arrived in Japan on Monday after helping CSKA Moscow to the Russian Cup on Saturday.
His cross was handled in the area by full-back Matt McKay in stoppage time and the bleach blond attacker stepped up to leather the spot kick straight down the middle past Mark Schwarzer to send the crowd into raptures.
"It's a shame we could not get a win but I am glad we have sealed qualification for the World Cup," Honda was quoted as saying by Kyodo.
"It was a little bit unfortunate that we went behind and there was not a lot of time left. But I spoke to Shinji (Kagawa) and we said we should keep forcing it and try to create space.
"Lucky for us we were able to get a penalty and I was able to put it away."
The result moved leaders Japan on to 14 points from seven matches in Asian qualifying Group B, meaning they are assured of top spot and reaching the 2014 finals with a game to spare.
Japan lie five ahead of Oman - who beat Iraq 1-0 in Muscat - and seven ahead of Australia, who moved above Jordan on goal difference with both sides having played a game less.
Japan finish their campaign against bottom side Iraq on Tuesday before they take on hosts Brazil in the Confederations Cup on June 15 with full back Yuto Nagatomo eyeing a bigger prize in South America.
"Keisuke showed how mentally strong he was today and I never doubted (he would score)," said the Inter Milan defender.
"I'm pleased but the real aim for all of us is to win the World Cup and this is just one step of that journey."
Japan missed their first opportunity to qualify for the finals in March when they slumped to a shock 2-1 loss away to Jordan and they were roared on by 62,172 fans at the Saitama Stadium desperate for their side not to waste a second chance.
Honda, back in the side after a thigh injury, and Kagawa caused the visitors all sorts of problems in the opening stages as Japan threatened to cut loose.
The Socceroos recalled veteran defender Sasa Ognenovski to partner experienced captain Lucas Neill in the centre of defence and the duo sat very deep, inviting Japanese pressure.
Honda, Kagawa and Yasuhito Endo all were close to scoring in the first 20 minutes but Ryoichi Maeda was quiet in attack as Japan's lack of a world class striker was evident again.
The second half continued in the same fashion as Kagawa clipped the crossbar in the 60th minute and Nagatomo wasted a good break with a tame effort in the 80th minute from the left.
The Socceroos made them pay for their wastefulness when Oar was the beneficiary of another error by Kawashima but Honda came to the rescue with a late equaliser that means they will take part in a fifth consecutive finals.
"I'm just relieved and happy," said Kawashima.
"It's a pity we conceded a goal like that but it happens in World Cup qualifying games like this. I'm just really happy that the team made it today at home in Japan."
The result aided Australia's hopes of taking the other qualifying spot in the group, with the top two in Group A also reaching Brazil directly, but Socceroos coach Holger Osieck was slightly disappointed not to have snatched a smash and grab win.
"Before the game a draw would have been good but when you are that close ... of course a draw is a little bit disappointing," Osieck told Fox Sports.