The result means Whincup hasn't missed the podium in five races since a rare DNF in Adelaide.
He's also won three of them, recovering lost points to re-join the title race.
Lowndes will also rejoice in his point-scoring podium finish since Sydney in 2016.
As it has been all weekend in Tasmania, race pace was ferocious.
Four drivers went below the previous race lap record, which is now held by Scott Pye after his 51.2622 second effort. Pye started seventh on the grid but failed to cash in after stalling during his pit stop.
David Reynolds continued his early-season momentum with fourth place, while Kiwi Fabian Coulthard was the biggest mover through the field, starting 11th but finishing fifth.
Commodores filled 11 of the top 13 places.