Cahill struck just before the hour and in the 77th minute after Japan's Brazilian-born defender Tulio ended Australia's seven-game streak of clean sheets with a header in the 40th.
The result left Australia on top of the group with 20 points, five more than Japan. They conceded only one goal in eight matches and were unbeaten in their final round of qualifying.
"I think it's a great statement to the rest of Asia and probably the rest of the world that you can finish a campaign like this five points ahead," Australia coach Pim Verbeek told reporters.
"We did not lose one game. We got one goal (against us). Can't have it all, but I think it's fantastic and I'm very proud of the players."
"He's so dangerous in the penalty box ... It's fantastic for the team to have a player like that, that you know he can always do what he has to do - score goals," Verbeek said.
Cahill's brace will have brought back painful memories for Japan fans who saw the attacking midfielder score two late goals to help Australia clinch a rousing 3-1 comeback victory in their group match at the 2006 World Cup in Germany.
