Prior to the race all of the riders had been instructed to change their bikes on the ninth or 10th lap after Bridgestone announced that it was unable to guarantee the safety of its rear tyres beyond 10 laps following resurfacing work on the Phillip Island track.
With the race reduced from 27 laps to 19 as a consequence, it was Yamaha rider Lorenzo who coped best with the unusual circumstances as he won convincingly from pole position to breathe new life into a title battle that seemed to be petering out.
Honda rider Marquez came into the race knowing victory allied to Lorenzo finishing third or lower would hand him the title in his debut season, but instead he saw his lead reduced to 18 points with two rounds remaining after earning a black flag for failing change his bike on schedule.
Marquez's team-mate Dani Pedrosa was the first of the front-runners to pit at the end of lap nine while Lorenzo followed a lap later, but Marquez did not peel off until lap 11, earning him disqualification for "exceeding the maximum number of laps before having to pit in".
Marquez's error allowed Lorenzo an untroubled run to the flag, with Pedrosa coming home in second place to maintain his own title hopes, with the Spaniard now 34 points off the leader.
Lorenzo's team-mate Valentino Rossi completed the podium, with British duo Cal Crutchlow and Bradley Smith fourth and sixth respectively on the Tech 3 Yamahas, sandwiching Alvaro Bautista (Gresini Honda) in fifth.
"I'm really happy with this win, we've also been lucky because Marc made this mistake," said Lorenzo. "Without that he would have been second or first because he was really fast today.
"So we've been lucky but we were unlucky in the middle of the championship so today is a balance.
"Now we have options, if Marc keeps constant on the podium then it is impossible to win the championship but there are a lot of laps to go so anything could happen."