The 18-year-old Mercedes driver was three tenths faster than his teammate, Briton George Russell, in second place.
Arvid Lindblad once again had a strong qualifying session. The Briton, who has a Swedish father, came tenth in his Red Bull car, beating, among others, Max Verstappen of Red Bull, who finished eleventh. The four-time world champion has had a tough start to the season.
Japan's Formula 1 race will be held on Sunday morning, local time in Sweden.
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