Boutros-Ghali was a controversial Egyptian politician and diplomat who headed the UN for only one term, with his renewal blocked by the US, the first time in the UN's history.
"We have been informed that the former secretary-general Boutros Boutros-Ghali has passed away," Rafael Ramirez, Venezuela's ambassador and this month's Security Council president, told the council.
Ambassador Ramirez asked members to rise for a moment of silence after making the announcement at the start of a meeting on Yemen's humanitarian crisis.
The 15 council members stood in silent tribute.Egyptian President Abdel Fattah al-Sisi reportedly phoned Boutros-Ghali on Thursday, after he was admitted to the hospital over a broken pelvis, to thank him for his work on behalf of Egypt and to wish him a speedy recovery.
The Egyptian diplomat is likely to be best remembered as the secretary-general whose second term was blocked by a US veto.
The veteran diplomat headed the world body from January 1992 until December 1996, during one of its most difficult times with crises in Somalia, Rwanda, the Middle East and the former Yugoslavia.
Boutros-Ghali was criticised for the UN's failure to act during the 1994 Rwandan Genocide, which left over one million people dead.
He also appeared unable to muster international support in the UN for intervention in the continuing Angolan Civil War.
In 1946, Boutros-Ghali graduated from Cairo University, where he was appointed professor of international law and after receiving his PhD from the University of Paris three years later.
The Egyptian academic's political career developed during the reigns of late President Mohamed Anwar al-Sadat and ousted President Mohamed Hosni Mubarak.
He served as Egypt's foreign minister from 1977 until early 1991, during which he played a significant role in the peace agreements between President Sadat and Israeli Prime Minister Menachem Begin.