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Earlier this week, Young had released a letter addressed to his manager and record label, Warner Music Group , demanding that Spotify no longer carry his music because he said Rogan spreads misinformation about Covid-19 vaccines.
On Wednesday, the 76-year-old Heart of Gold and Rocking In the Free World singer thanked his record label for "standing with me in my decision to pull all my music from Spotify," and he encouraged other musicians to do the same.
"Spotify has become the home of life threatening Covid misinformation," he said on his website. "Lies being sold for money."
The Swedish company said it worked to balance "both safety for listeners and freedom for creators" and had removed more than 20,000 podcast episodes related Covid-19 in accordance with its "detailed content policies."
"We regret Neil's decision to remove his music from Spotify, but hope to welcome him back soon," Spotify said in a statement.
Rogan is the host of "The Joe Rogan Experience," the top-rated podcast on Spotify, which holds exclusive rights to the programme.
The 54-year-old has stirred controversy with his views on the pandemic, government mandates and vaccines to control the spread of the coronavirus.
Earlier this month, 270 scientists and medical professionals signed a letter urging Spotify to take action against Rogan, accusing him of spreading falsehoods on the podcast.
Young said Spotify accounted for 60% of the streaming of his music to listeners around the world. The removal is "a huge loss for my record company to absorb," he said.