There will also be an expanded eight-team finals series made up of seven matches.
Just a month ago there was concern about Japan's ability to field a team due to to a stand-off between the national organisation and clubs over player payments, however SANZAR confirmed their entry.
The Rebels travel to Tokyo in round four in March, although the Japanese franchise is still to reveal how many of their national team, who recently upset South Africa in the World Cup, will take part.
They and Argentina will reveal details of their franchises after the World Cup, although Japan confirmed they will split their games between Tokyo and Singapore.
A new stadium is being built in Buenos Aires to host matches.
Australia's best performing teams, the NSW Waratahs and Brumbies, face tough opening matches.
The Brumbies take on last year's losing finalists the Hurricanes in Canberra on February 26, while the Waratahs host old foes Queensland Reds a day later with the Western Force and Rebels also meeting that day.
Australian Rugby Union chief executive Bill Pulver said the arrival of Japan and Argentina to Super Rugby would expose the game and competition to a new supporter base. "We know there is an enormous appetite for the game in Japan with an estimated 20 million Japanese fans tuning in to the Rugby World Cup so far, spurred on by the national team's stunning upset of South Africa."
Pulver believed Australian teams would again challenge for the title. "When you look across the board at the Australian teams, every one of our teams at full strength can make a strong push for the finals." AAP