The race-leading No. 912 Manthey EMA Porsche 911 GT3 R had been hit with a drive-through penalty as heavy rain arrived at Mount Panorama.
Ayhancan Guven was leading the race as a safety car for an accident by the Invitational class-leading No. 10 Matt Stone Racing IRC GT put the field under neutralization for the seventh time.
All of the cars pitted for wet-weather Pirelli tires, with Matt Campbell, back in the Manthey EMA Porsche, re-taking the lead although was later deemed to have completed a stop quicker than the 85-second minimum pit lane delta time.
Campbell was served with a drive-through penalty on the restart, although the Australian served it while under another safety car, for an incident by Paul Tracy in another Invitational class entry.
The German squad, including Head of Porsche Motorsport Thomas Laudenbach was seen in the pit lane pleading their case that the penalty was correctly served, although race officials stated that the penalty must be served under green flag conditions.
The drama has given the lead to the No. 13 Phantom Global Racing Porsche of Bastian Buus, while still running under the safety car.
The No. 2 Melbourne Performance Centre Audi R8 LMS GT3 Evo II of Ricardo Feller, meanwhile, was hit with a two-minute stop-and-hold penalty penalty due to contact with the No. 10 MSR car, which was served just prior to the latest safety car.