The Belgian driver entered the rally just three points behind Ogier in the closest title fight in 15 years. He held the upper hand on his French rival, building a near-10 second gap through the first five stages at Coffs Harbour before hitting a chicane and finishing the stage with only three tires on his Hyundai.
Neuville was fortunate the puncture occurred late enough in the day to finish all six forestry stages and avoid a retirement. But the mistake cost him 40 seconds and gave Ogier, who is 33 seconds ahead of him, a clear run at his sixth straight championship.
In his last start with Ford before a move to Citroen next year, Ogier struggled as the first to drive the dusty, slippery forest routes. "I pushed like crazy, I was on the limit over the jump and everywhere, I can't do (any) more," Ogier said. "I was on the limit."
With Ogier on sweeping duties the back markers flourished, and Mads Ostberg took the lead in his return to the series. Ostberg was forced to miss the previous round in Spain to make way for rally winner and nine-time world champion Sebastien Loeb, who was making the last of his three guest appearances for Citroen.
Now back in the seat, Ostberg leads Jari-Matti Latvala by 6.8 seconds in the Australian rally, with sixth-stage winner Craig Breen in third. Ogier was seventh, 38.2 seconds off the pace, but only needs to finish ahead of Neuville to claim the championship title. Neuville is in 10th place after six stages.
Roles will reverse on Saturday, with Ogier to start further back in the field and do his best on cleaner roads to make up the day-one deficit before Sunday's final stages. Andreas Mikkelsen, the 2016 Rally Australia champion, was an early dropout after rolling into a ditch in his Hyundai. Mikkelsen had only just avoided a tractor that had found its way onto the course.
Former winner Molly Taylor and co-driver Malcolm Read were also forced out of their event when their Subaru hit a hay bale at high speed on the morning's second stage. Both reported soreness but suffered no serious injuries.
The 24-stage rally totals 319 kilometers (197 miles). Ten stages are scheduled Saturday with the final six on Sunday, most of them through forests on the New South Wales state's north coast about 530 kilometers (325 miles) north of Sydney.
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