Six-time MotoGP world champion Marc Marquez grabbed pole position for the first time in three years as he defied wild weather in qualifying for the Japanese Grand Prix on Saturday.

On a badly disrupted day of heavy rain and lightning at Motegi, the world title contenders struggled to master the conditions.

Spanish great Marquez had no such trouble however on his Honda with his leading time of one minute and 55.214 seconds, ahead of France's Johann Zarco, 0.208 seconds behind, and South Africa's Brad Binder (0.323 sec).

The weather is forecast to be considerably better on Sunday for Japan's first MotoGP since 2019 because of the pandemic.

The 29-year-old Marquez, who was also fastest in a wet second practice, last took pole more than 1,000 days ago, again in Japan.

This was his 63rd MotoGP pole and comes with him only recently back from yet another bad injury.

"Really happy to be on pole today," he said, adding it was "really important for me... to achieve this small target".

But he cautioned: "Tomorrow in the dry will be a different race and different story."

Of the trio of title challengers, Spain's Aleix Espargaro was best-placed at sixth on the grid for Aprilia, with reigning world champion Fabio Quartararo ninth on his Yamaha.

Francesco Bagnaia, who has slashed Quartararo's championship lead to 10 points with five races left in the season, was a disappointing 12th on his Ducati.

- 'No pressure' -

There are just 17 points separating the top three in the title race.

Enea Bastianini is also mathematically still in it, but he will start the race in 15th after crashing his Ducati on Friday and again in qualifying.

The Italian, victorious last week at Aragon, called it "another negative day".

But he is not giving up on his slim title hopes.

"I will do my best to recover the gap. In front of me I have a lot of fast riders and I can use this to close this gap," he said.

But the day was all about Marquez.

He only returned to action last weekend, having been on the sidelines since June when he underwent an operation in the United States on his right arm, which was fractured in a crash in July 2020.

It was the fourth time he had gone under the knife for the injury.

Marquez said his physical condition meant he "can't go full attack" on Sunday and he played down any hope of victory, but he is enjoying riding without pressure.

"No pressure means even if I finish on the second row, it's OK," he said.

"But I knew the feeling of this morning (when he was fastest in practice), there was a good chance to make a good qualifying."