Kiwi Brendon Hartley will start the Japanese Formula 1 Grand Prix from a career-best sixth place after a stunning qualifying performance.

The Le Mans winner out-performed his Toro Rosso teammate Pierre Gasly and four-time world champion Sebastian Vettel at his engine supplier Honda's home event, much to the delight of the Japanese fans.

Both Hartley and teammate Gasly took grid penalties for introducing new engines at last weekend's Russian Grand Prix in order to be in the best shape possible for Japan. Both cars were forced out of the race early in Sochi as they battled brake issues.

The Toro Rosso cars have struggled in recent times as other cars in the mid-pack have undergone upgrades.

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Despite the struggles, Hartley was feeling good about Japan even prior to qualifying after a recent upgrade to his Toro Rosso's Honda engine, which he said could lead to a strong result at the Suzuka circuit.

"I am still optimistic we could have a strong end to the year if everything comes together," he said before today's qualifying round.

Reigning world champion Lewis Hamilton will start from pole alongside his Mercedes teammate Valtteri Bottas after they made the right decision to get out early in Q3 and set a fast early lap because rain impacted on the Ferrari pair of Vettel and Raikkonen later in the session.

Both had a chance early but failed to put down a fast lap.

With five races to go, Hamilton leads Vettel by 50 points in the standings.