The 29-year-old Briton, winner of the last three Grands Prix, was fastest with a late lap at the new Sochi Autodrom to finish two-tenths of a second clear of his Mercedes team-mate and title rival Nico Rosberg.
The German, 10 points behind Hamilton in the championship with four races remaining, pushed hard to catch him, but was almost overhauled by Finn Valtteri Bottas in the final seconds, the Williams driver only missing out on a front row start when he slid off circuit at the penultimate corner.
"Pole is a great place to start and the team have done a great job," said Hamilton.
Briton Jenson Button recovered from an undistinguished showing in Saturday morning's final free practice to take fourth place on the grid alongside Bottas.
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Local favourite Daniil Kvyat claimed a rousing fifth place for Toro Rosso to the delight of a capacity crowd in the Olympic Park circuit. It was the 20-year-old Russian's best qualifying performance.
Qualifying too place on a beautiful late summer's day in the Black Sea resort in contrast to the lashing rainstorms a week earlier in Japan, where Frenchman Jules Bianchi suffered his life-threatening injuries last Sunday.
The two Mercedes men were soon on top with solid laps as the scramble to survive the first cut began. Bottas was soon on their heels, but Felipe Massa struggled with fuel pressure problems and was eliminated in 18th place.