The Radiohead frontman and his friend the influential producer-musician initially put "Amok" up on the service but decided after six months to take the unusual step of pulling it down.
Yorke wrote: "Make no mistake new artists you discover on #Spotify will no get paid. meanwhile shareholders will shortly being rolling in it. Simples."
Streaming payment models have gotten more attention as the mobile-friendly services continue to grow, taking a larger piece of the music marketplace.
At a Spotify gathering last month in New York to tout a staffing increase, Ken Parks, the company's chief content officer, said the company has already paid $500 million in royalties and was scheduled to reach $1 billion by the end of 2013.
The company released a statement Monday morning noting, "Much of this money is being invested in nurturing new talent and producing great new music. We're 100% committed to making Spotify the most artist-friendly music service possible and are constantly talking to artists and managers about how Spotify can help build their careers."
Yorke and Godrich who say the decision only applies to the Atoms album, Yorke's solo record "The Eraser" and Godrich's Ultraista project and not the Radiohead catalog say they're standing up for their fellow musicians. They believe popular artists with large catalogs probably are seeing some return.
"Meanwhile small labels and new artists can't even keep their lights on. It's just not right," Godrich wrote.
AP Writer Jennifer Peltz in New York contributed to this report.
Follow AP Music Writer Chris Talbott: http://twitter.com/Chris_Talbott.