Batemans Brewery said the name was similar to its Yella Belly Gold ale, which was named after the “yellowbellies" nickname for Lincolnshire locals.
The dispute is under review by the European Union Intellectual Property Office (EUIPO).
In an Instagram post, Omnipollo said it had been “forced to discontinue” the 11% peanut butter and biscuit-flavoured imperial stout, which was introduced in 2014.
“After several attempts to come to an agreement, the European trademark owner didn’t see a way for us to exist,” a later post said.
The Swedish brewery said it would continue to sell the product in the US and “regroup” on the European market. “Don’t hate, innovate,” it added.
Yellow Belly has distinct white packaging - a reference to white supremacist group the Ku Klux Klan - and is named after the colour yellow’s connotations with cowardice.
It was the result of a collaborative project between the Derbyshire and Stockholm-based breweries.
Buxton Brewery describe the beer as being “meant to be enjoyed as a celebration of all things new, open-minded and progressive”, as well as political commentary.
Batemans’ 3.9% blonde beer Yella Belly has been brewed for around two decades, its managing director said.
Stuart Bateman said the brewery had tried to “negotiate a solution” after explaining its protected registration but had heard nothing from the other breweries.
He added: “Batemans has been brewing Yella Belly Gold for some 20 years, initially as a pale ale flavoured with Madagascan vanilla pods.
“The name was chosen to reflect our Lincolnshire roots as a family business that has been brewing in Wainfleet since 1874.
“Long story short … Yella Belly Gold has been a long-standing, popular and successful brand for Batemans."
Geoff Quinn, owner of Buxton Brewery, told the BBC it was a shame to discontinue its beer, but said it hoped to avoid "legal wrangles which wouldn't really benefit anyone".
"We don't see how we could get accused of passing off our beer as their's or vice-versa," he added.
The number of new trademarks for beer brands increased by 20% in 2017 due to a craft beer boom, research from law firm RPC showed.