The 29-year-old had been expected to slot back into his old team, the Queensland Reds, after returning home from a stint with Parisian club Stade Francais.
But last week, Genia cast doubt on a return to the team where he won the 2011 championship under coach Ewen McKenzie, citing the Reds’ full complement of scrumhalves.
Salary cap issues may also have played a part, with Genia’s deal worth about A$800,000 (484,376.45 pounds) a season and with payment to be split between the Australian Rugby Union (ARU) and the Rebels, according to local media.
Genia was frank that the Reds were his first choice.
“Yeah, it’s the unfortunate nature of the situation, that’s where I always wanted to go back and play but that’s just the circumstances that we were given, I guess, because I did come back at such an awkward time,” he told reporters at a Wallabies training camp in Sydney on Tuesday.
“At the end of the day, I’m happy with my decision… I don’t have any bad sort of feeling towards the Reds, I’m happy.”
The 78-test veteran instead joins a team that finished bottom of the Australian conference with a solitary win and was only recently assured of continuing in the competition next season after a protracted process to cull a local side.
The ARU said in April it would axe either the Rebels or the Western Force as Super Rugby scales down from 18 teams to 15 next year, but the governing body only announced its decision to remove the Perth-based side last Friday.
The Force are still fighting to remain, however, and have lodged an appeal with the Supreme Court of New South Wales which will be heard next week.
The Rebels are yet to make the playoffs since joining the competition in 2011 and endured a terrible, injury-blighted most recent season as players toiled under the threat of an uncertain future.
The team is looking for a new coach after former Munster boss and Wallabies assistant Tony McGahan ended his four-year tenure at the end of the regular season.
Force coach Dave Wessels has been linked with the role, if the Perth team loses its legal fight and is dissolved.
Earlier this month, former owner Andrew Cox handed the Rebels’ licence back to the sport’s state governing body, the Victorian Rugby Union, in a move both parties claimed had secured the team’s future.
The Rebels have since announced a raft of new signings, with former Wallaby Tetera Faulkner crossing from the Force on a two-year deal and Japan number eight Amanaki Mafi taking a one-year extension.
Genia, who has captained the Wallabies a number of times and played at the 2011 and 2015 World Cups, is expected to start in Michael Cheika’s side in the Rugby Championship opener against the All Blacks in Sydney on Saturday.
(Reporting by Ian Ransom; Editing by Greg Stutchbury)