It was the worst moment of a difficult day for Mercedes, whose other driver Nico Rosberg had stopped at the end of the first session with an engine problem.
Sauber's Sergio Perez,
who will replace Hamilton at McLaren next season
following the Englishman's decision to move to Mercedes, narrowly avoided a similar incident when the Mexican also put two wheels on the grass on the entry to Spoon but managed to stay on the track.
His team-mate Kamui Kobayashi also had a heart-stopping moment when he ran wide in the high-speed Dunlop corner but managed to rejoin.
The litany of incidents underlined Suzuka's well deserved reputation as one of Formula 1's toughest tests, but there were no major incidents in the 90-minute session.
"Why is the Kers not working?" Raikkonen asked his team over the radio.
Japan GP Second Practice
1. Mark Webber - Red Bull 1:32.193
2. Lewis Hamilton - McLaren 1:32.707
3. Sebastian Vettel - Red Bull 1:32.836
4. Nico Hulkenberg - Force India 1:32.987
5. Fernando Alonso - Ferrari 1:33.093
6. Romain Grosjean - Lotus 1:33.107
7. Jenson Button - McLaren 1:33.349
8. Bruno Senna - Williams 1:32.499
9. Felipe Massa - Ferrari 1:32.614
10. Michael Schumacher - Mercedes 1:32.750
His engineer replied: "We have a Kers problem, we have to treat the car as unsafe at the moment."
Raikkonen returned to the pits and was only able to get out on to the track with a little over five minutes remaining.
Alonso arrived in Japan with a 29-point championship lead over Vettel, who is 16 points ahead of Raikkonen, with Hamilton a further seven adrift.
The Spaniard's Ferrari looked uncompetitive in the first session but he was much quicker in the second, setting the fastest time straight out of the pits, from Hamilton and Vettel.
"We can be reasonably happy," said Vettel. "The car seems to be improving. There are still some things we need to improve so we need to do another step overnight. Tomorrow it will be very close.
"We had a good day. This morning the car was very nervous but this afternoon seemed to be quite a bit better. I was a lot happier, and both [tyre] compounds we seemed to perform reasonably well."
"It looks pretty competitive at the front," said BBC F1 technical analyst Gary Anderson. "I'd like to pat Hulkenberg on the back - that's a good effort by him."
Both Ferrari and Red Bull had problems with blistering of their rear tyres - where the surface of the rubber overheats and bubbles.
Anderson said it looked like quite a serious problem on both cars.
But Vettel said he was not concerned about it.
Button on top in Suzuka practice 1
"Generally the track is quite hard for the tyres," he said, "because there are a lot of high-speed corners one after the other so there is no time of the tyre to rest. We did a lot of laps, at some stage it is natural the tyres start to go off and you start to slide around. But I think overall we can be quite happy."
It was unclear immediately whether McLaren were suffering similar problems, as they would be expected to if their main rivals were in such trouble.
Hamilton and Button were running different set-ups, with more downforce on Hamilton's car.
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