Youngster Euan McLean came in between the sticks in place of the Pole, as Mark Kerr and Jordan Robertson both dropped to the bench.
But Hamilton, who had just started his final hot lap, comfortably eclipsed that mark to take his eighth career pole.
If the race finishes as it starts then third place will be enough for McLaren's Lewis Hamilton to hang on to his lead in the title race (124 pts) from the two Red Bulls of Mark Webber (121 pts) and pole-sitter Sebastian Vettel (115pts).
But the curator of a National Museum of Wales exhibition to mark the centenary of Scott reaching the South Pole, believes that the Welsh obsession with polar exploration had very little to do with the nation's pioneering spirit, or even the charismatic Robert Falcon Scott.
BBC: Scott of Antarctic 'propaganda created Welsh obsession'
The world champion set pole position with a lap 0.641 seconds faster than second placed Mark Webber of Jaguar.
The 54-year-old became the second-oldest driver to start on the pole in a Sprint Cup car, a few months short of Harry Gant's mark.
Red Bull's Sebastian Vettel took pole ahead of Hamilton and Alonso, whose closest championship rival, Vettel's team-mate Mark Webber, was fifth.
Just 0.087 seconds separated the top four as the Pole headed McLaren's Lewis Hamilton, Ferrari's Fernando Alonso and Red Bull's Mark Webber.
With team-mate Felipe Massa qualifying third, half a second behind Alonso and pole-sitter Sebastian Vettel, and ahead of the German's Red Bull team-mate Mark Webber, it was Ferrari's best qualifying result of the season so far.
His mark soon disappears though as right behind him, Massa posts 1:29.329 to take pole in Turkey for the second straight year.
BBC: SPORT | Motorsport | Formula One | Turkish GP qualifying as it happened
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