Stoner came into the weekend looking to win his home race and started well by securing pole on Thursday ahead of his Spanish rival.
But the Honda star's cause was further boosted when Lorenzo hurt his finger after crashing in the warm-up and was forced out of the race, with his Yamaha stablemate Ben Spies also pulling out.
Australian Stoner - who has won the last four races at Phillip Island - just needs to finish in the top six to reclaim the Moto GP title.
Yamaha said of Lorenzo: "He will travel to Melbourne to undergo plastic surgery to repair the damage.
"A post surgery report will follow."
Honda man Marco Simoncelli moves to second on the grid with Suzuki's Alvaro Bautista third.