In front of a surprised crowd, the Wallabies star left the field as soon as the first stoppage in play, straight after the kick-off at Hanazono Rugby Stadium in Osaka yesterday.
Kintetsu made the unusual move due to the competition rules, which state a player must feature in at least one game of the regular season to be eligible for the two-legged Replacement Battle.
The Wallaby star, who was returning after rupturing his achilles tendon in August, was not hurt in contact and left the field unaided, with a quizzical look on his face.
Although Cooper is now eligible for his side's first game of the promotion/relegation series on May 7, the ploy didn't help Kintetsu as they tumbled to a 43-26 defeat against the NEC Green Rockets, for whom former Wallaby halfback Nick Phipps was a try-scorer.
The loss confirmed Kintetsu's place as Division One wooden spooners.
This means Cooper, and his long-time halves partner Will Genia, now face former Test teammate Israel Folau in the survival contest, after Urayasu D-Rocks beat Wallaby fullback Tom Banks' Mie Honda Heat to secure top seeding from Division Two for the series.
Folau was also on the comeback trail, having not played since mid-January, but he made a successful return, playing the final 30 minutes for D-Rocks.
Despite two tries from Banks, Urayasu maintained their unbeaten record for the season.
Former Wallaby flanker Liam Gill matched his countryman's effort, with his double leading D-Rocks to a convincing 48-28 win.
The third of the relegation ties will see Matt Toomua and Curtis Rona's Mitsubishi Heavy Industries Sagamihara Dynaboars play Toyota Industries Shuttles Aichi.
The former Wallaby pairing and their Dynaboars teammates will take some confidence into that series after recovering from a 24-point halftime deficit against Ricoh Black Rams Tokyo.
Sagamihara closed to 24-21 before former England loose forward Nathan Hughes scored his third try of the game to get the Black Rams home 31-21.
The Fijian-born Hughes, who is now eligible for his homeland, has been in dominant form and scored nine tries in his final five games of the season, to put himself on the radar of Fiji coach Simon Raiwalui.
At the top of the table, Wallaby winger Marika Koroibete was a try-scorer as Saitama Panasonic Wild Knights beat Toshiba Brave Lupus Tokyo 34-22 to eliminate Todd Blackadder's team from the playoffs, while securing top seeding for Robbie Deans and his men.
The first semi-final is on May 13 where Saitama will play Springbok Faf de Klerk's Yokohama Canon Eagles, who beat Kobelco Kobe Steelers 52-26.
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