The headquarters was located underground, beneath residential buildings in the Dahiyeh, the IDF said.
Footage of the enormous blast was circulated on Lebanese media and the attack is being reported as the heaviest in Beirut in almost a year of conflict between Hezbollah and Israel.
Hezbollah’s al-Manar television reported that four buildings were destroyed and there were many casualties.
Prime Minister Benjamin Netanyahu was interrupted during a briefing with Israeli reporters after his speech at the United Nations.
The Israeli PM could be seen listening to his military secretary Maj. Gen. Roman Gofman, who whispered in his ear minutes before he ended the press briefing and left with his advisers.
The attack comes after Israel has eliminated much of the Hezbollah senior leadership in recent weeks.
In a statement, IDF Spokesman Rear Adm. Daniel Hagari said the Israeli Air Force struck Hezbollah’s main headquarters but did not mention whether Nasrallah was a target or was believed to be present at the site.
On Friday afternoon, Hagari said: “Moments ago, the Israel Defence Forces carried out a precise strike on the Central Headquarters of the Hezbollah terror organization - that served as the epicenter of Hezbollah's terror.
“Hezbollah's central headquarters was intentionally built under residential buildings in the heart of the Dahieh, in Beirut, as part of Hezbollah's strategy of using Lebanese people as human shields.
“After almost a year of Hezbollah firing rockets, missiles, and suicide drones at Israeli civilians, after almost a year of Israel warning the world and telling them that Hezbollah must be stopped, Israel is doing what every sovereign state in the world would do if they had a terror organization that seeks their destruction on their border, taking the necessary action to protect our people so that Israeli families can live in their homes, safely and securely.”