SID news agency said the payment is the largest in the charity's history.
"Three years ago, an individual donated 100,000 euros to us," board chief Margret Hartkopf told Tagesspiegel newspaper.
She said the foundation was "totally surprised" when the court announced that Ecclestone's settlement would involve the 83-year-old paying $99 million to Munich authorities and $1 million to the charity within one week.
While the payment will make Ecclestone a free man, however, that does not mean the Gerhard Gribkowsky corruption affair is over.
APA news agency reports that Ecclestone has also offered to compensate the Munich state bank to the tune of EUR 25 million, but first BayernLB must agree to the proposal by Friday.
The report said BayernLB, whose spokesman was not commenting on Wednesday, was earlier pushing for compensation in the realm of hundreds of millions of euros.
And DPA news agency reports that Ecclestone's $100m payment also does not include the settlement of related criminal proceedings against his former right-hand man, lawyer and F1 board member Stephen Mullens.
Prosecutors claim Mullens, who left F1 in 2011, helped Ecclestone to make the disputed millions in alleged bribe payments to the jailed Gribkowsky.