Haraguchi got Japan off to a flying start by scoring in the fifth minute at Docklands stadium but the visitors' celebrations were tempered when the midfielder made a clumsy challenge on forward Tomi Juric shortly after the break.
Socceroos captain Mile Jedinak slotted home the spot-kick in the 52nd minute to salvage a point for the hosts but both the Asian heavyweights were left frustrated after chances went begging in a high-tempo second half.
The result left each team with their World Cup destiny in their hands, but Japan will leave more satisfied after shrugging off fatigue and injury concerns to hold the Asian Cup champions.
"My feeling after this game is not regret, maybe some frustration," Japan coach Vahid Halilhodzic told reporters.
"We had a tactical preparation based on our physical condition.
"The players did a good job, especially defensively."
Australia coach Ange Postecoglou started Juric up front, with veteran forward Tim Cahill playing the last 20 minutes off the bench.
Talisman Cahill, the match-winner against Japan at the 2006 World Cup, was loudly cheered by the crowd of 48,000 when he came on but was unable to influence the game.
Australia paid the price for an early mistake by defender Trent Sainsbury.
Keisuke Honda laid off a superb pass for Haraguchi to run on to and he finished with a deft left-foot shot that slid beneath keeper Mat Ryan's outstretched leg.
Rattled, Australia lifted their work-rate but were devoid of ideas going forward in a sluggish first half.
They were lucky not to be 2-0 down in the 28th minute when Honda, afforded space at the edge of the area, fired straight at the keeper.
A more enterprising Socceroos team emerged after the break, and were rewarded when Haraguchi fouled into Juric in the box.
Jedinak hammered his spot kick straight down the centre.
A brilliant, diving save by Ryan denied Yu Kobayashi in the 74th minute, the keeper's right glove stopping the midfielder's header.
Japan also endured a nerve-jangling finish, with defender Matthew Spiranovic latching on to a free kick from Massimo Luongo but sending the header over shortly before stoppage time.
"We were very poor in the first half," Postecoglou said. "That’s a major disappointment for me."
(Editing by Ed Osmond)
