People magazine said the gift will be divided evenly between Save the Children and the International Rescue Committee.
"By allowing us to make their generous donation to Syrian children public, Sacha and Isla are helping highlight the tragedy of the issue today," Justin Forsyth, chief executive of Save the Children, said in a statement Sunday.
IRC President and CEO David Miliband said their "great expression of humanity" was "an example to many others seeking practical ways of making a difference during the Christmas and New Year season."
Cohen and Fisher have been married since 2010. They have three children.