Kiwi driver Van Gisbergen, who won Saturday's race, finished fifth after a run-in with Volvo's James Moffat on lap 48.
Moffat was issued a drive-through penalty for his role in the accident, which cost him a top 10 finish.
Defending series champion Mark Winterbottom has relinquished third place in the title standings to Lowndes after completing a shocking weekend with a 14th-placed finish.
Van Gisbergen was rapt after winning on Saturday and keeping Whincup stuck on 99 wins.
"I made one mistake at turn one and had to defend, but other than that, it was pretty cool, I enjoyed that one," the New Zealander said.
The next round of the championship is the Sandown 500 on September 18.