The archbishop made the call in response to Islamic State's violent attacks in Iraq and Syria.
He also said that "protecting the inalienable dignity and value of every human" must come above following other laws or social norms, and that this process shouldn't be viewed as forcing a country's agenda onto another or limiting a country's ability to govern itself.
Archbishop Bernardito told the UN: "The responsibility to protect is a recognition of the equality of all before the law, based on the innate dignity of every man and woman.
"The Holy See wishes to reaffirm that every state has the primary duty to protect its own population from grave and sustained violations of human rights and from the consequences of humanitarian crises.
"If states are unable to guarantee such protection, the international community must intervene...
"The Holy See hopes that the alarming, escalating phenomenon of international terrorism, new in some of its expressions and utterly ruthless in its barbarity, be an occasion for a deeper and more urgent study...of our common responsibility to protect people from all forms of unjust aggression."
Islamic State has declared that it is enslaving women from the Yazidi community, a religious minority found in Iraq and Syria, among other countries.
The Muslim extremist group has also released an article stating that it wants to "conquer Rome" and enslave Catholic women.