The members of the Femen movement entered the Gothic cathedral dressed in long coats which they whipped off inside while ringing three bells near the altar.
"Pope no more!" they cried. "No more homophobe" and "Bye bye Benedict!" Scandalised visitors voiced their disapproval.
"This is a sacred place, you can't strip here," said a Frenchwoman. The Femen women's power group has been making headlines since 2010 for topless feminist, pro-democracy and anti-corruption protests in Russia, Ukraine and London.
The protesters were dragged out of the cathedral by security but remained outside for some time shouting "In gay we trust" and "Get out homophobe."
Stephane Lemessin, a Catholic priest and columnist for France's Catholic newspaper La Croix (The Cross), called the group's actions "stupid".
"It is absolutely ridiculous what they did," Lemessin told the Local.
Scores of Twitter users also took to the social media site to express their outrage at the group with the hashtag #Femen being one of the top trending throughout the morning.
"If you are really that courageous go and do the same thing in a mosque," tweeted @tepauvrefrance, echoing the thoughts of many on Twitter.
"Femen, have you nothing better to do than provoke poor Catholics on a subject that does not concern you?" tweeted @bobbymhan
Tuesday's bare-all protest is not the first time the feminist groups have provoked the wrath of the Catholic church.
Last year members of the group dressed up as nuns to try to sabotage an anti-gay marriage protest in Paris. The women ripped off their 'habits' to reveal comments scrawled on their naked chests such as "In gay we trust" and F##k the church".
They also fired canisters of tear gas at the marchers.
Some members of the feminist group were attacked and injured by the marchers. Five people have since been arrested in connection to the violence.
Catholic group Civitas then sued the group for “sexual exhibitionism” in front of children, as well as protesting illegally and insulting a religious group by mocking their appearance.
Alain Escada, the president of Civitas, said the catholic group would also be suing Femen for spreading a message in a violent manner, organised violence with arms and threatening the freedom to protest of others.