The couple made the donation through their Jolie-Pitt Foundation earlier today, which would have been Pearl's 43rd birthday.
The couple's representative, Trevor Neilson, tells People magazine, "On this day our thoughts go out to Danny's family.
"The Daniel Pearl Foundation is celebrating this day, his birthday, with music festivals around the world. The festivals are a great reminder of not just Danny's work as a journalist but of his life and his love of music."
The Mr. and Mrs. Smith stars and their three children arrived in India last week to film the movie, after security concerns prevented them from making it in Pakistan.
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