Van Gisbergen and Kostecki finished today's opening Perth race first and second respectively following a heated battle between the pair.
The Kiwi ran down Kostecki in the closing laps, the latter receiving a bad sportsmanship flag for blocking, while the former instigated contact numerous times while trying to get past.
That included contact as part of the race-winning pass at turn 6, something that Erebus has now formally protested.
The formal protest follows a request for an investigation from Erebus that was subsequently dismissed by officials following the race.
“Motorsport Australia stewards have received protest paperwork regarding the result of race 7," said a Motorsport Australia spokesperson. "A hearing will be held on Sunday morning.”
The protest comes despite calls from both van Gisbergen and Kostecki, and Erebus boss Barry Ryan, for less intervention from race control when there's a one-on-one battle for the lead.