The 30-year-old tighthead, who was part of the front row that did much to repair the reputation of Australia's scrum at last year's World Cup, signed a three-year deal to move to the Top 14 club last year.
"President Laurent Marti and Sekope Kepu have today agreed to cancel the contract that runs until June 2018," Bordeaux-Begles said in a statement on their website.
"This resolution was entered into after a request from the player to return to Australia for family reasons. The two parties part on very good terms and we wish Sekope Kepu good luck with the rest of his career."
Kepu is in camp with the Wallabies preparing for the June test series against England, qualifying under the "Giteau Rule" that allows players with more than 60 caps to continue representing Australia despite being based overseas.
The New South Wales Waratahs later announced the 63-cap Wallaby had signed a three-year deal to resume his Super Rugby career in Sydney, where he played for eight seasons until his France move.
"I'm delighted that Keps is returning to Australia, and happy to welcome him back to the Waratahs," Waratahs coach Daryl Gibson said.
"He will be a great addition to the squad and will strengthen our front row options."
Kepu's front row combination with hooker Stephen Moore and loosehead Scott Sio gave Australia a stability up front they had not enjoyed for years as they won the Rugby Championship and reached the World Cup final last season.
(Reporting by Nick Mulvenney; Editing by John O'Brien)
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