It comes just three months after he was confirmed to have inked a contract extension with the team.
"I will be parting ways Brad Jones Racing at the end of the 2021 Supercars Championship season," he wrote in a statement.
"This has been a difficult decision to make.”
Percat will now be on the lookout for a new team for the first time since 2016, when he left Lucas Dumbrell Motorsport for BJR.
Walkinshaw Andretti United looms as a major suitor, with Percat’s greatest successes coming with the Clayton organisation.
Walkinshaw Racing signed a teenage Percat in 2007 and backed him when he claimed the 2009 Formula Ford title in dominant fashion.
Percat stepped up to the Supercars development series in 2010 and finished fourth overall, before finishing seventh in 2011.
That year, he combined with Garth Tander to win the Bathurst 1000 on his first attempt, becoming only the second rookie to win the Great Race.
After further enduro campaigns with Tander in 2012 and 2013, Percat made his full-time debut in 2014 when James Rosenberg took his Racing Entitlements Contract (REC) to operate a car out of the Walkinshaw Racing operation.
He scored a Sydney Motorsport Park podium before finishing a sensational third in Bathurst, marking his second Great Race podium in four years.
Percat would not only push WAU team leader Chaz Mostert, but enhance the squad’s teams’ championship push.
After seven rounds in 2021, Mostert is just eight points from third overall. Meanwhile, teammate Bryce Fullwood is only 15th.
Percat won Bathurst for the Walkinshaw-led HRT
Mostert re-signed with WAU just weeks before Percat’s BJR extension was announced, and Fullwood’s 2022 plans haven’t been locked in.
With Percat now a free agent, 13 of the 25 seats for 2022 have been filled.
Only Red Bull Ampol Racing, Shell V-Power Racing Team, Erebus Motorsport, Team Sydney and Blanchard Racing Team have locked in their full 2022 line-ups.
Seats remain at Kelly Grove Racing, Tickford Racing, Team 18 and Matt Stone Racing.
A shift to either Kelly Grove Racing or Tickford Racing would prove a major change for Percat.
Percat made his main game debut in 2010, and has made all 242 career starts in Commodores.
As it stands, only 2020 Super2 champion Thomas Randle has been confirmed at Tickford, which will expand to four cars next season.
Walkinshaw gave Percat his full-time debut in 2014
Cameron Waters is likely to remain with the Ford team, which leaves two Tickford seats to be filled.
Neither Jack Le Brocq or James Courtney have yet to be confirmed with the Ford squad.
Tickford is no stranger to sticking established drivers in one of its seats.
Since its championship debut in 2003, Tickford has employed the veteran likes of Craig Lowndes, Jason Bright, Will Davison and Lee Holdsworth.
Percat will turn 34 next September; Lowndes (28), Bright (32), Davison (28) and Holdsworth (36) had all accrued genuine winning experience before they made their Tickford debuts.
David Reynolds (Kelly Grove Racing) and Mark Winterbottom (Team 18) haven’t had their 2022 teammates confirmed, although Scott Pye is expected to be retained by the latter.
That leaves Matt Stone Racing, which is also expected to retain its 2021 line-up of Jake Kostecki and Zane Goddard.