كتب : وكالات
The Everton midfielder struck twice in the final six minutes before John Aloisi sealed the win for the "Socceroos" in injury time.
Shunsuke Nakamura had put Japan in front through a controversial goal in the first-half.
The win, which is the first for Australia in World Cup history, put them temporarily atop their Group F on three points ahead of Brazil's game against Switzerland on Tuesday.
Australia had the upper hand early in the first half as Japan keeper Yoshikatsu Kawaguchi was called into action to deny Mark Viduka's two attempts to break the deadlock.
In the 24th minute, Mark Bresciano received Viduka's back-heel pass on the edge of the area before firing, but Kawaguchi continued his impressive display with a brilliant save.
Just two minutes later, Nakamura put Japan ahead when his cross went over Australia keeper Mark Schwarzer into the empty net.
Television replays showed that Schwarzer was impeded by Atsushi Yanagisawa while attempting to clear.
Egyptian referee Essam Abdul-Fattah allowed the goal amid protests from Australia's players.
The game was brought down to pedestrian pace up until Cahill registered the equalizer for the Aussies, also their first goal in World Cup history.
Cahill slotted home amid a forest of legs in the 84th minute when Kawaguchi failed to control a long throw-in in the Japanese area.
In the 89th minute, Cahill rifled a long-range shot to grab the lead for Australia before Aloisi drilled a left-footer home to seal the win in injury time.
Australia next face Brazil while Japan, featuring in their third successive finals, on June 18th.