The Japanese headed into the third and final match day lying in fourth place and needed a bonus point victory to secure the title. That decisive try came deep in injury time to deny Tonga and send the Japanese players, officials and fans into a frenzy of celebration.
Samoa, scheduled to meet Wales in Hamilton on September 19, lost to arch rivals Tonga 29-19.
"This is big for Japan Rugby and Fiji gave us the chance as their discipline let them down," said Japan coach, John Kirwan.
"However, I salute my players for the effort and they did what I asked them at the break. Now it is the World Cup and there is still a lot of work to be done."