Formula One's governing body said the 25-year-old lost control of his Marussia on the wet track, travelled across the runoff area and hit the rear of a recovery tractor which was trying to remove a stricken Sauber.
The accident led to the race at Suzuka being stopped and cast a pall over the paddock with drivers shocked at what had happened.
McLaren's Jenson Button, who finished fifth, said it was "an accident that you hope never happens in Formula One".
Bianchi, extracted unconscious from the car, was taken by ambulance to Mie General Hospital where he underwent surgery.
"The CT scan shows that he has suffered a severe head injury," the International Automobile Federation (FIA) said in a statement.
Speaking to France 3 television, Bianchi's father Philippe said it could take 24 hours before the situation became clearer.
The accident was the most serious involving a driver at a grand prix weekend since Brazilian Felipe Massa suffered near-fatal head injuries in Hungary in 2009 after being hit on the helmet by a bouncing spring shed from a car in front.
Massa made a full recovery from that incident and was racing for Williams on Sunday.
The Brazilian, who has the same manager as Bianchi, went with other drivers and team officials to the hospital after the race while an outpouring of support for the Frenchman flooded social media.
Bianchi, a graduate of Ferrari's young driver academy, scored Marussia's first ever points when he finished ninth at this year's Monaco Grand Prix and was highly-rated with a bright future.
The accident occurred at the same point of the track, the Dunlop Curve, where Adrian Sutil had aquaplaned off into the tyre barrier moments earlier (lap 42) and was watching his car being removed.
The crash brought out the safety and medical cars and then the red flags.
MUTED PODIUM
There were no podium celebrations and the champagne was left unsprayed, with the top three drivers merely clinking the bottles before putting them back on the ground.
"It's obviously a real anti-climax to hear that one of our fellow colleagues is seriously injured so that's really the main worry," Mercedes' race winner Lewis Hamilton told the BBC.
"You could see some commotion and the car was really badly damaged on the right. We just hope he's OK."
"I'm not thinking about the race, I'm thinking about my colleague," said his team mate and title rival Nico Rosberg. "I've been given some information and it seems very, very serious. I'm hoping for the best."
Nice-born Bianchi, who comes from a motor racing family, is a regular travelling companion of Ferrari's double world champion Fernando Alonso and popular with other drivers, with whom he often plays soccer.
Formula One is proud of its safety record, and constantly strives to make cars safer, while remaining acutely aware that the sport will always be dangerous.
"Motor-racing is dangerous. We get used to it if nothing happens and then suddenly we are all surprised," former champion Niki Lauda, who came back from a near fatal crash in 1976, told reporters.
The death of Brazilian triple world champion Ayrton Senna, in 1994, remains the last driver race fatality but there have been close escapes since then.
Marussia's former test driver Maria De Villota, who died last year, lost her right eye and fractured her skull when the Spaniard's car accelerated into the back of a parked team truck at a 2012 test in England.
(Writing by Alan Baldwin; Editing by John O'Brien and Pritha Sarkar)
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