Rev Canon James Allison, 57, from St John the Baptist Church in Coley near Halifax said some members of the congregation had "issues" about the practise. which has Hindu and Buddhist roots.
Referring to the church's parochial church council, he told the South West News Service (SWNS): "We had a meeting and took the unanimous decision not to renew the yoga class agreement in the hall.
"Yoga is a rainbow of different experiences and some of our congregation have issues with some styles and teachings."
Instructor Melissa Makan said she had been using St John the Baptist for her yoga nidra sessions for the last seven months when she received a text "out of the blue" asking her find a new location.
The 37-year-old was quoted by the SWNS as saying: "It's ridiculous.
"Yoga isn't a religion. If I could explain it to him, or he could come and see it for himself, but they haven't tried to understand it.
"My style and my teachings have zero Sanskrit words, it has no mantras, the language is completely clean and that's because I'm personally not religious.
"What he is doing is causing a division when the world is already so divided, he is openly saying that's ok. I just think, 'what are you representing?'"
The Church of England does not exercise a blanket ban over yoga classes on church premises, the MP who represents the Church of England in the House of Commons said last year.
Dame Caroline Spelman said the Church offers guidance on what activities to allow - but churches can exercise "discretion" over whether they allow yoga sessions.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.