Nevada-based Hindu activist Rajan Zed led the protest to have the beer discontinued.
"Breweries should not be in the business of religious appropriation, sacrilege, and ridiculing entire communities," he said in a statement.
"It was deeply trivializing of divine Hindu deity to be displayed on a beer can."
The beer was a New England-style double IPA that was a part of a series of deity-themed beers. Other beers included "Aqua Jesus" and "Aqua Buddha."
"We deeply apologize to the Hindu community for this poor choice of our beer name and artwork," the breweries said in a joint statement released by Zed.
"We simply did not put enough time into thinking about this beer name and artwork and what the use of the name Shiva means to the Hindu community."