Ecclestone has bought 3,000 tickets at an average price of 35,000 yen (£295) for a three-day pass for the Suzuka circuit.
It is a mark of his generosity after more than 15,000 people were killed in the wake of the tsunami that followed an 8.9-magnitude earthquake that struck the Fukushima prefecture.
Ecclestone, who turns 81 at the end of this month, has also allowed a glove puppet to be commissioned of himself, with all proceeds, at a cost of £29, going towards tsunami charities.
The puppet, which is around 12 inches in height, carries a shock of his trademark wispy white hair, with Ecclestone winking behind a pair of stitched-on glasses.
Further funds are to be raised via the auctioning of paintings of each of the five currently active reigning and former world champions - Sebastian Vettel, Jenson Button, Lewis Hamilton, Fernando Alonso and Michael Schumacher - and their cars in which they won the title.
Button and Hamilton have also joined in the fund-raising as they are to auction off their helmet and boots that have been specially designed for this weekend's race, with the Japanese flag serving as inspiration.
Children Without Borders will benefit from Hamilton's sales, whilst money from Button's lots will go to Save Japan.