Late in the race, Chaz Mostert rear-ended Rick Kelly, sending him to the gravel for the second straight race.
The Tasmanian meet concludes with a final 200-kilometre race today.
Earlier, Lowndes was hit by his own team-mate and the stewards in a tough day at Symmons Plains. In race one, the V8 Supercars championship and race leader was hit by Whincup in a robust move, losing the lead and eventually finishing eighth.
Then a stewards' inquiry ruled Lowndes had to start the next race from the back of the grid after tape was found over a hole his car's rear window during qualifying. The penalty was applied because the tape constituted a safety issue and gave Lowndes a slight aerodynamic advantage.
It's far cry from the veteran Red Bull racer's outlook halfway through race one when he led the race and was looking forward to a second front-row start in race two.
Whincup said the pair's bump was "unfortunate" but he had no regrets over his passing move: "I feel like I haven't done anything wrong. We've been mates for 10 years and hopefully that can continue."
Team owner Roland Dane struggled to hide his frustration: "I can sympathise with both of them, I'm just annoyed it's between both our cars. They know not to do that and it won't be happening again."
Stewards are yet to rule on the legality of Whincup's passing move but have announced an investigation.
Courtney placed second in race one with Ford's Winterbottom third. Russell Ingall, who qualified third fastest, held off Volvo's McLaughlin for fourth place.
- AAP