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Hamilton was then given a drive-through penalty by stewards for forcing another car off the track while Massa was also hit with the same penalty for his collision with the young Briton. There was additional disappointment for McLaren when Kovalainen's race came to an end after he pulled to the side of the track when smoke began emanating from the back of his car.
Hamilton entered the pits on lap 18 for his drive-through penalty while Massa followed suit soon after. Upon rejoining the race, Hamilton was 15th, while Alonso was showing significant pace and climbed to second by lap 26 before taking the lead when his team-mate Piquet entered the pits.
Giancarlo Fisichella was then out of the race after problems with his car forced him back into the pits. Having made another pit stop in lap 43 Hamilton rejoined the race before overtaking Honda's Rubens Barrichello to move into 12th spot.
However, Massa was showing real pace as he climbed into the points three laps later and then set the fastest time in lap 50 with a time of one minute 18.963 seconds. But the Brazilian then made contact with Bourdais in the following lap causing him to spin before recovering.
Massa was tenth by lap 54 but once again set a new fastest time three laps later and then passed Nick Heidfeld for ninth. Piquet dropped out of the chase for second leaving Kubica and Raikkonen to battle it out while Alonso was comfortably in first place.
Massa managed to squeeze inside of Webber to ensure eighth place while Kubica came out on top for the battle for second, leaving Alonso to secure a stunning victory.
With two races remaining the two-time world champion admitted his two successive victories give him confidence of further podium finishes.
"I don't know what to say," said Alonso. "My head says yes as the feeling I have now is that we can do anything. Who knows maybe podiums are possible now."
Kubica, meanwhile, was delighted to secure second on the podium to keep himself still in the hunt for the world championship.
"Qualifying was crucial. I managed do to get a good result. Finishing second is a very good result for the team. It is difficult at the moment as everyone is pushing."
Result of Japanese Grand Prix:
1 Fernando Alonso (Spa) Renault one hour 30 minutes 21.892 seconds
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