It came after protests from both Tickford Racing and Walkinshaw Andretti United were lodged.
Triple Eight quickly confirmed its intention to appeal.
A hearing was heard in Melbourne on Wednesday, a week before the Beaurepaires Melbourne SuperSprint.
A three-person panel comprising Walter Sofronoff KC, Steve Chopping and Ross Jackson made the decision based on the hearing.
The hearing went for over three hours, with Triple Eight's appeal heard and later dismissed.
Motorsport Australia judicial update - appeal hearing
Motorsport Australia can confirm Triple Eight Race Engineering’s appeal has been heard and dismissed and cars 97 and 88 are disqualified from race one of the Newcastle 500.
Tonight’s hearing was held in Melbourne at Motorsport Australia House in Canterbury, beginning at 6pm and concluding at 9.30pm.
A three-person panel was convened to hear the appeal. The three members are Walter Sofronoff KC, Steve Chopping and Ross Jackson.
A full and substantiative decision paper will be published by close of business on Friday and posted on the Motorsport Australia website in full.
In a team statement, Triple Eight said it was "disappointed" in the decision to uphold the disqualification.
However, the team "respects the outcome delivered by the Supercars National Court of Appeal".
Triple Eight statement
Triple Eight are disappointed in the decision to uphold the team's disqualification of both cars from Race 1 of the Newcastle 500 for a technical breach.
The team maintains our position that we were given an instruction allowing us to install the cooling boxes in a place that conferred no performance advantage at all, but respects the outcome delivered by the Supercars National Court of Appeal.
Our sole focus now shifts to the upcoming Melbourne 400 [SuperSprint], and the remainder of the 2023 Supercars Championship season.
It ensures WAU Ford driver Chaz Mostert will take a 45-point series lead to next weekend's Beaurepaires Melbourne SuperSprint.
Coca-Cola Chevrolet driver Brodie Kostecki is second ahead of Monster Ford star Waters.
Van Gisbergen and Feeney remain 11th and 18th in the standings, 126 and 165 points behind Mostert respectively.
The 2023 Repco Supercars Championship will resume at the Beaurepaires Melbourne SuperSprint on March 30-April 2.