Winterbottom sent the Red Bull Holden sliding into the Turn 10 barrier on just the 15th lap of the 74 lap contest after Lowndes had pulled off a successful pass at the previous corner.
The hit with the tyre wall damaged the left-rear corner of Lowndes' Holden, which could then not be fully refuelled at its second pitstop.
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The situation comes just one event after an aggressive move from Winterbottom bundled Lowndes out of the Race 32 lead at Phillip Island.
On that occasion a ‘no breach of rules' verdict from stewards was met by a Dane protest, which was subsequently thrown out.
“For sure if he had of not had a DNF we would have been protesting him,” Dane told SEN radio.
“It absolutely goes against what the stewards have told us this year.
“It was careless driving and I'm just amazed at the lack of any steps being taken against him over it. But he's had a DNF and I couldn't care less.”
Winterbottom said he was in unsure of how the incident with Lowndes occurred.
“I don't know what happened,” he told Speedcafe.com.
“I will have to look at the vision. I might have got a tap from behind. It seemed to accelerate suddenly.”
At the driver's briefing there was a suggestion that race stewards would take a more liberal approach to aggressive driving for the finale.
Dane took a dim view of the suggestion, saying that rules are there to be enforced.
“You have to have rules in sport,” he said.
“What are you going to do go into the grand final and smash people around the head as much as you want. It shouldn't happen here either.
“We should be encouraging people to keep it clean here and not dirty.”
Winterbottom was given an injection prior to the race after suffering from a bout of tonsillitis, but says he will “absolutely” return for Sunday's race, despite now being out of title contention.