The car was qualified by Rick Kelly, and they started from 8th position on the grid.
Alex Davison and Rick Kelly rounded out the top ten.
He recovered, but he lost the series lead to Rick Kelly, who took a handy 73-point lead.
Rick Kelly was given a drive-through penalty, and finished 18th.
Steven Johnson was shortly afterward put into the wall after contact with Rick Kelly.
Whincup had another disappointing race and left the weekend with his championship lead almost halved, 81 points ahead of Rick Kelly.
Rick Kelly scored the team's first race win in wet conditions at the Hamilton 400.
Rick Kelly won the 2006 series.
Lowndes was a contender for the championship right up until the last race, being level on points with Rick Kelly.
The protest was dismissed after a long hearing and Rick Kelly was confirmed as the 2006 champion.