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Hamilton clocked a time of one hour, 39 minutes and 40.382 seconds, finishing 2.581 seconds ahead of Vettel.
Renault-bound Daniel Ricciardo was sixth in the second Red Bull, but his session was brought to an abrupt early end when he pulled off and parked.
A fading signboard along theYamuna Expressway that once directed fans arriving for Indian Grand Prix to their section of the track, with a worn-out Formula One logo as its centrepiece.
Hamilton questioned the strategy of taking Formula One to places like India, Korea and Turkey where the sport did not survive for long.
The four-time champion German, who finished second behind Red Bull’s Max Verstappen in the Mexican Grand Prix, said he wanted to win another title by beating the best opposition.
Hamilton’s success, the third time he has taken the title without finishing on the race podium, elevated him to a supreme club with only seven-time champion Michael Schumacher ahead of him.
Hamilton now leads Vettel by 70 points and with 75 remaining in the final three races he can clinch his fifth title by finishing seventh in Mexico, if Vettel wins.
Hamilton needs to beat fellow-four-time champion Vettel by eight points to clinch his fifth drivers championship.
The Ferrari ace was reported to the stewards for not slowing sufficiently when the rain-hit opening practice was red-flagged after Charles Leclerc had brought gravel back on the circuit.
Hamilton was speaking on the sidelines of the United States Grand Prix where on Sunday he can become just the third driver to win the F1 world title five times.
Valtteri Bottas held off Max Verstappen to take second almost 13 seconds behind Hamilton in a breathless 53-lap race at the fast-flowing Japanese circuit.
'Never in a million years': Lewis Hamilton grabs 80th pole at Japanese Grand Prix as Sebastian Vettel flounders
Vettel skidded off twice in his desperation to set a time and his starting position of eighth will be his lowest of a season which began so brightly but looks like ending in bitter disappointment.
The Formula One championship leader pushed his Mercedes to a time of one minute, 29.599 seconds, just over a tenth quicker than Ferrari rival Sebastian Vettel.
The runaway Formula One championship leader appears to have complicated that task by refusing to rule out leaving Mercedes when his current contract expires in 2020.
It was Hamilton's third win in Russia, his fifth in six races and the 70th of his career, confirming he has the momentum to clinch a fifth title triumph with five races remaining.