Renault's Robert Kubica and Mercedes' Nico Rosberg were next, ahead of Webber, Force India's Vitantonio Liuzzi and Alonso.
Force India's Vitantonio Liuzzi was 15th, but lucky to escape without injury after crashing into the pit wall.
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Sakon Yamamoto, Adrian Sutil, Sebastian Vettel, Takuma Sato and Liuzzi are the others.
BBC: SPORT | Motorsport | Formula One | Turkish GP qualifying as it happened
Klien was replaced by Vitantonio Liuzzi for the next three races but the rules prevented him from driving in practice.
Force India test driver Vitantonio Liuzzi said the tires were "amazing", providing excellent grip compared to the grooved tires currently used.
Mallya is convinced his team will continue to be strong for the remainder of the season, with reserve Vitantonio Liuzzi expected to replace Fisichella.
However, Italian Vitantonio Liuzzi and Germany's Hulkenberg, who raced for Williams last year before making way for Venezuelan Pastor Maldonado, are also under consideration.
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Last month they dropped American Scott Speed in favour of German Sebastian Vettel with immediate effect, and now Bourdais will replace Italian Vitantonio Liuzzi.
The second session was initially stopped after Force India's Tonio Liuzzi careered of the track because of aquaplaning caused by the huge volume of water on the circuit.
Along with Liuzzi it was the six drivers from the new teams Lotus, Hispania and Virgin who bowed out after Q1 with Lotus' Jarno Trulli the quickest of them.
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Vitantonio Liuzzi earned two points for the Mercedes-powered Force India team with ninth, and former Brawn driver Rubens Barrichello took the final point with 10th on debut for Williams.
It compounded a miserable weekend for Schumacher, who was overtaken at the very end by the Force India duo of Vitantonio Liuzzi and Adrian Sutil to finish out of the points.
Liuzzi's German team mate Adrian Sutil, who had suffered a driveshaft failure in final practice, qualified 14th but will be demoted five places on the starting grid for an unscheduled gearbox change.
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Toro Rosso, who have not scored any points so far this season, have yet to name their second driver for 2008 amid speculation that triple ChampCar champion Sebastien Bourdais could replace Vitantonio Liuzzi.
The first qualifying session was stopped early on when Force India's Vitantonio Liuzzi smashed into the wall at Turn 17, losing control after running wide on the last corner and touching the artificial grass.
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The driver line-up is not yet known, but Austrian Christian Klien, who got the Jaguar seat last season due to his Red Bull sponsorship, and Italian youngster Vitantonio Liuzzi, who Red Bull backed to the Formula 3000 title this season, are among the candidates.
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Although Renault have said they are also considering former Force India driver Vitantonio Liuzzi, and intend to give third driver Bruno Senna some time in the car on Sunday, they made it clear that if Heidfeld impressed them on Saturday, the drive was his.
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