Mostert was kicked out of the first of three sprint races after the team illegally used a battery-operated air blower on the grid.
The breach of regulations was admitted to during a hearing earlier this evening.
However, since the ruling was handed down, the team has decided to appeal the penalty.
"Walkinshaw Andretti United has lodged a notice to appeal tonight’s decision to disqualify car 25 from Race 16," read a statement from the team.
"The team will not be making any further comment at this stage."
According to the stewards report the breach was considered a technical infringement, the blanket penalty for which is disqualification.
"Given that in this case the breach resulted in a potential sporting advantage for car 25 at the start of Race 16, the stewards are satisfied that no other penalty would be appropriate in this case," the report read.
Mostert had finished fourth in the race behind Dick Johnson Racing pair Anton De Pasquale and Will Davison, and Triple Eight's Shane van Gisbergen.
While Mostert isn't considered a genuine title contender at this point, his disqualification will be a hit for WAU in the teams' championship.
This is his second disqualification in as many days after he was tipped out of Practice 2 for a breach of the minimum tyre pressure regulations.
A further hearing on this latest matter isn't expected until at least next week.
