Entitled "Gemeinsam sind wir stark" - German for "Together we are strong" - the instrumental, which has no lyrics, was released over Christmas.
The anthem drew close to 180,000 views on YouTube, and surged on Amazon.de's music chart to become its bestselling MP3 download, knocking Adele's "Hello" to number two.
The release of the track on Amazon sparked a storm of criticism, with the online retailer coming under fire for making money from its sales.
PEGIDA, an acronym for Patriotic Europeans Against the Islamisation of the Occident, had said profits from the sale would be given to homeless Germans.
But Amazon placed a message on its German webpage, saying profits from its sale would be donated to help hundreds of thousands of migrants, many fleeing the Syrian civil war, who have arrived in Germany over the past year.
"Amazon's profits from the sale of this song will go to a non-profit-making organisation supporting refugees," the company said.
PEGIDA started life over a year ago as a xenophobic Facebook group, initially drawing just a few hundred protesters to demonstrations in Dresden.
Interest initially waned after founder Lutz Bachmann posted "selfies" showing him sporting a Hitler hairstyle and moustache but it revived as around a million asylum seekers arrived in Germany this year alone.
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