A post to Stewart's official Facebook page says the veteran rocker, who played St. John's July 11, is upset with how the widely shared photograph is being used.
Before performing on Saturday night, the British singer was fitted for the coat at Always in Vogue on Water Street.
The move garnered praise from local residents, and on the flip side, an attack from anti-sealing activist Paul Watson.
On Tuesday, a post to Stewart's Facebook account said he was not being fitted for a sealskin jacket and had no intention of purchasing the item.
"Rod regrets that he didn't check what the jacket was made of, but was so grateful for the shop's help, he did not," the post read.
"Rod has since been very upset to learn that the shop has been using this image as an advertisement for an industry that he does not know much about and certainly does not support."
'Just like one of the guys'
Always in Vogue owner Darren Halloran told CBC News over the weekend that Stewart's visit to his downtown shop was a pleasant surprise.
"I explained to him that we make everything in house and showed him some of the stuff that we do, and we just had a nice chat," Halloran said Monday. "He was just like one of the guys."
He added, "At the end of it, we did have them all fitted for sealskin jackets, that was my request, and they loved them."
The Facebook post claims a store clerk at Always in Vogue asked Stewart to pose with one of the store's jackets before leaving.
Stewart also tweeted that he was "enraged to learn that an image of me has been misused for something I do not support."