Fenwick has removed the cartoon image from its ten department stores across the country, saying it never meant to upset shoppers.
In a statement, spokesman Nigel Poulton said: "On reflection, this greeting card has been removed from display and de-listed.
"It is definitely not our intention to cause offence to any customers."
The £1.99 card, which shows a clergyman looking into the pan of the toilet and shouting an expletive, was withdrawn after customers at the Fenwick branch in Canterbury complained.
Rev Simon Tillotson from All Saints Church in Whitstable, Kent told the Sun: "It's beneath a shop like Fenwick to be selling a card like that.
"They've done the right thing removing it."
One shopper told the newspaper: "A card featuring a vicar in such a situation might be amusing in the right context.
"But, frankly, it's offensive in a family store", he added, while another said: "It's very bad taste, indeed".