Martin extends championship lead with Australian MotoGP sprint win
Italy's defending world champion Bagnaia could only come fourth, with Spaniard Marc Marquez second and another Italian, Enea Bastianini, completing the podium in third.
Fabio di Giannantonio was fifth and Franco Morbidelli sixth on a day marred by a huge crash between Maverick Vinales and Marco Bezzecchi.
Vinales appeared to get caught in Bezzecchi's slipstream late in the race, making contact that sent the riders and bikes barrelling into the gravel.
They both appeared to be OK, just battered and bruised.
Ducati star Bagnaia won the sprint and main event in Japan two weeks ago to close the gap with Pramac rider Martin to just 10 points.
But Martin surged to pole in Australia for a third consecutive year and on an overcast and cool day on Phillip Island proved unstoppable.
The win improved his lead to 16 points ahead of the grand prix on Sunday and with just three race weekends left after Australia.
Six-time world champion Marquez moved up to joint third in the standings, 84 points behind Martin, alongside Ducati's Bastianini.
Martin had the perfect start, unlike Marquez on his Gresini who went wide at the first corner and slipped from second to eighth as Bagnaia moved up to fourth.
Neither could catch Martin, who streaked away to open a 2.6sec lead at the halfway mark and cross the line 1.520sec clear.
It was the first-ever 13-lap sprint race at Phillip Island after last year's planned race was cancelled because of bad weather.
