Lowndes tapped the rear of Waters' Monster Energy Falcon at Turn 7 which forced him wide and allowed the Triple Eight driver through.
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Stewards elected to defer the investigation to the next event with officials at Phillip Island deeming Lowndes was at fault.
The veteran admitted to a charge of careless driving, which would normally spark a five-second penalty if issued during a race.
Despite being hit with the penalty Lowndes remains seventh in the championship standings.