Winterbottom told Speedcafe.com that he had been pushed off the track at Turn 2 by Lowndes while the pair battled in wet conditions following the second Safety Car restart.
Prodrive submitted an official protest, which is required within 30 minutes of the finish and must be accompanied by a $4,000 fee, which is returned if the protest is upheld.
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Stewards have confirmed that they will hear the protest at the next round of the championship at Sandown.
The tap from Lowndes was compounded by subsequent contact from Andre Heimgartner, which damaged Winterbottom's steering and resigned the championship leader to a 16th place finish.
“He hit me hard in the back. I just got sent off,” Winterbottom told Speedcafe.com of Lowndes.
“Lowndes put me wide, sent me off the track and then Andre (Heimgartner) cleaned the steering up.
“I was just holding on from there. It was disappointing because the car wasn't too bad but once the steering was bent that was it.”
Lowndes currently sits third in the championship, 255 points behind leader Winterbottom.