The drama arose after both Counties and Akarana fielded players contracted to the Warriors' New South Wales Cup side, which last year came under the umbrella of the Auckland Rugby League when the team was known as the Auckland Vulcans.
This season saw the Warriors' NSW Cup players registered with the NSWRL, meaning they were not officially registered with the ARL, resulting in those players being ineligible to take part in the National Premiership.
"With the disappearance of the Vulcans it's only now that we're realising it's creating a void in terms of the processing of the eligibility," Holden said.
Friday's ruling comes after the Bulls won their place in the final on Wednesday, after they successfully protested against Counties for fielding an ineligible player in their regular-season fixture last month.
Counties won that game, but lost the competition points to slip out of the final, before launching their own protest against second-ranked Akarana for the same offence.
Both Auckland teams now miss out, while Wai-Coa-Bay and Canterbury must hurry their travel arrangements and attempt to focus their attentions on Saturday night's match.