The 25-year-old Frenchman passed away Friday night at the hospital in Nice, southeastern France, where he was admitted following the October 5 accident, a family statement said.
"Jules fought right to the very end, as he always did, but today his battle came to an end," said the Bianchi family. "The pain we feel is immense and indescribable."
Bianchi's death is the first resulting from a Formula One Grand Prix accident since that of Ayrton Senna in San Marino in 1994.
The team for which he raced -- Marussia, now known as Manor F1 -- tweeted that it was "devastated to lose Jules after such a hard-fought battle."
Team leader John Booth described Bianchi as a "shining talent" who was destined for great things in the world of motorsport and was "a magnificent human being."
"Words cannot describe the enormous sadness within our team this morning, as we come to terms with losing Jules," he said in a statement posted to Facebook on Saturday.
"He has left an indelible mark on all our lives, and will forever be part of everything we have achieved, and everything we will strive for going forward."
Fellow Formula One driver Jenson Button paid tribute to "a truly great guy and a real fighter."
The official Twitter account for Formula One voiced condolences to Bianchi's friends and family via Twitter, also referencing the young driver's chosen race number - 17.
Bianchi's family thanked all those who had been involved in his care, both in Japan immediately after the crash, and later in France.
"Furthermore, we thank Jules' colleagues, friends, fans and everyone who has demonstrated their affection for him over these past months, which gave us great strength and helped us deal with such difficult times," the statement said.
"Listening to and reading the many messages made us realize just how much Jules had touched the hearts and minds of so many people all over the world."
In December, the sport's world governing body, the FIA, published a report
which stated that Bianchi "did not slow sufficiently
to avoid losing control" during his crash at the Suzuka circuit.
In the days after the crash, the Marussia said it was "shocked and angered" by claims Bianchi had not reduced his speed and that the team had actively encouraged him not to do so.