The decision was taken after failed attempts to have six South African teams, instead of five, accepted into the competition.
ARU announced earlier this year they wanted the Kings to be given their chance in the Super 15, and they admitted it was likely to be at the expense of another franchise. It was announced on Thursday the Lions have been relegated after finishing bottom of the South African Conference this year.
The decision means the Kings will join the Cheetahs, the Bulls, the Stormers and the Sharks in the Super 15, while the Lions will be given their chance to regain a spot via a two-legged relegation/promotion play-off at the end of the 2013 season.
"All rugby provinces have been consistently in support of the need for an Eastern Cape team in the Vodacom Super Rugby competition," said Oregan Hoskins, president of SARU.
"That decision was first taken in 2005 but their inclusion has twice been postponed.
"We made a commitment to the Kings to include them in 2013 and rugby has delivered on that commitment.
"The franchise represents more clubs than any other region - apart from the Stormers - and contains numerous leading rugby schools. It has been starved of top-class rugby competition for a decade and a half and now it has the chance to show what it can do."
The news was met with obvious unhappiness by the Lions.
"We are extremely disappointed at this result," said Lions president Kevin de Klerk. "This is a very unfortunate decision which will result in a team taking part in a competition without needing to qualify on rugby merits. We will take time to consider this decision and then to plan our response that best protects our players, staff, stakeholders and supporters."