Boys won Race 2 at Mount Panorama and took overall round honours; following the disqualification, he has dropped to 13th in the standings.
MW Motorsport's Tyler Everingham is the official Race 2 winner, with Tickford Racing's Zak Best the new series leader.
It comes after Triple Eight's Broc Feeney, who won Race 1, was penalised for an on-track incident.
Walkinshaw Racing issued a statement this morning saying:
"The reason for this understanding was due to WR's low-stock levels for rebuilds, following engine damage across all four Walkinshaw Racing Supercars engines at the 2020 Adelaide 500, sustained as a result of the new mandated engine package.
"This issue was heightened by the subsequent COVID-19 lockdown throughout 2020, which presented ongoing resource and parts supply issues.
"At no point was the decision to use the development cylinder head made for performance, the decision was made due to the availability of parts prior to and inclusive of a worldwide pandemic, and at all times, WR is of the belief that the engine was compliant due to the ongoing discussions and open dialogue with Supercars.
"It is disappointing that Image Racing and driver Jordan Boys have been disqualified from Race 2.
The series will resume at Winton Motor Raceway across May 29-30.