At least six people were killed and 91 were wounded, Lebanon’s health ministry said. It was the biggest blast to hit the Lebanese capital since Israel war on Lebanon in 2006 and appeared likely to push the escalating conflict closer to full-fledged war.
The death toll is likely to rise significantly as teams comb through the rubble.
Hezbollah's al-Manar television reported seven buildings were destroyed.
Israel claimed it was attacking Hezbollah's headquarters and weapons facilities, while US and Israeli media reported that the Lebanese Hezbollah leader Hassan Nasrallah was the target.
The fate of Nasrallah, leader of the resistance and political party for 32 years, remains unclear, although a source close to the group said he was "fine".
Earlier, a source close to Hezbollah told Reuters that Nasrallah was alive. Iran's Tasnim news agency also reported he was safe. A senior Iranian security official told Reuters that Tehran was checking his status.
After heavy shelling sounded across the Mediterranean city on Friday, Israel issued fresh warnings for people to leave part of the densely populated Dahiyeh suburbs before dawn on Saturday.
Hundreds of families spent the night on the streets, seeking shelter in downtown Beirut's Martyrs' Square or along the seaside boardwalk area.
Syrian refugee and father of six Radwan Msallam said they had "nowhere to go".
"We were at home when there was the call to evacuate. We took our identity papers, some belongings and we left," he told AFP.
The Israeli army declined to comment on Nasrallah but claimed on Saturday to have killed "Muhammad Ali Ismail, the commander of Hezbollah's missile unit in southern Lebanon, and his deputy" as well as "other senior officials".
Hours earlier at the UN General Assembly, Israeli Prime Minister Benjamin Netanyahu vowed to keep fighting Hezbollah until the country's border with Lebanon was secured.
Hezbollah began low-intensity attacks across the border a day after Israel launched its genocidal war on Gaza.
Israel has in the past days shifted the focus of its operation from Gaza to Lebanon, where heavy bombing has killed more than 700 people and sparked an exodus of around 118,000 people.
Five hours strikes
In the Haret Hreik neighbourhood, an AFP photographer saw the blasts left craters up to five metres (16 feet) wide. Ambulances careened into the area, while families scrambled out.
A second wave of attacks on the same southern suburbs followed on Saturday, as the Israeli army said it warned civilians to get away from three buildings in the heart of Dahiyeh.
Israel also announced strikes on the Beqaa area in eastern Lebanon and Tyre in the south.
Rarely seen in public, Nasrallah enjoys cult status among his Shiite Muslim supporters and is the only man in Lebanon with the power to wage war or make peace.
After five hours of continuous strikes on Beirut early on Saturday followed Friday's attack, the strikes appeared to stop around 6:00 am (0300 GMT), though fires were still smouldering in several areas.
"I felt like the building was going to collapse on top of me," said Abir Hammoud, a teacher in her 40s.
After the wave of strikes on Beirut, Hezbollah claimed a rocket attack on kibbutz Kabri in northern Israel, "defending Lebanon and its people".
The Israeli army said sirens sounded in the north.
Deadliest in a generation
Israel provided no immediate comment about the type of bomb or how many it used, but the resulting explosion levelled an area greater than a city block.
The Israeli army has in its arsenal 2,000-pound, American-made “Bunker Buster” guided bombs designed specifically for hitting subterranean targets, AP reported.
Richard Weir, crisis and weapons researcher with Human Rights Watch, said the blasts were consistent with that class of bomb, AP added.
Israel this week raised the prospect of a ground invasion in Lebanon, prompting widespread concern for an all-out regional war.
"We must avoid a regional war at all costs," UN chief Antonio Guterres told world leaders, while appealing again for a ceasefire.
In Israel, too, many were weary of the violence.
"It is incredibly exhausting to be in this situation. We don't really know what's going to happen, there's talk of a ground offensive or a major operation," said Lital Shmuelovich, a physiotherapy student.
In New York, Netanyahu also addressed the war in Gaza, saying that Israel's occupation army would continue to fight until it achieved "total victory".
Diplomats have said efforts to end the war in Gaza were key to halting the fighting in Lebanon and bringing the region back from the brink.
"The path to diplomacy may seem difficult to see at this moment, but it is there, and in our judgement, it is necessary," US Secretary of State Antony Blinken said.
Israel's genocidal war has killed at least 41,534 people in Gaza, most of them children and women, according to figures provided by the Palestinian health ministry. The UN has described the figures as reliable.
Change the rules
The violence on Lebanon has raised fears of spillover across the Middle East.
Netanyahu took aim at Iran in his UN General Assembly address, saying to Tehran: "If you strike us, we will strike you."
He added: "There is no place in Iran that the long arm of Israel cannot reach, and that's true of the entire Middle East."
Analysts have said Iran would try to resist being dragged into the conflict.
But following the Beirut strikes, Iran's embassy in Lebanon said: "This reprehensible crime... represents a dangerous escalation that changes the rules of the game."
Iran's President Masoud Pezeshkian later condemned the strikes, branding them a "flagrant war crime".
Lebanese Prime Minister Najib Mikati urged the international community to "stop" Israel from waging a "genocidal war" against Lebanon, following the Israeli strike on Beirut's southern suburbs.
"This new Israeli aggression proves that the Israeli enemy doesn't care about all the international efforts and calls for a ceasefire," Mikati, who is in New York, said in a statement issued by his office, urging the international community to stop the "genocidal war that it (Israel) is waging on Lebanon."
Israeli airstrikes on eastern and southern Lebanon have killed more than 720, including dozens of women and children, and wounded hundreds of others since Monday.
The United Nations said the attacks has displaced 211,000 people, including 85,000 now staying in public schools and other shelters. Israeli airstrikes have forced 20 primary health care centers to shut down and disrupted access to clean water for nearly 300,000 people.
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