Opposition leader Vojislav Kostunica has declared himself the new president. Speaking on state television on Thursday evening, he described the day as great moment in Serbian history.
The parliament building was earlier stormed and set on fire as security forces first tried to halt the demonstration with teargas and then switched sides. The state television and radio stations were also taken over.
The whereabouts of Mr Milosevic are not known - he has not been seen all day - but rumours that he has fled were fuelled by reports that three heavy aircraft had flown out of a military airport near Belgrade on Thursday evening, heading south.
Opposition spokesman Zoran Djindjic later said Mr Milosevic was in the southeastern town of Bor, 100km (60 miles) south of Belgrade, with his associates.
Yugoslav army chiefs were meeting in Belgrade early on Friday, reported the state news agency Tanjug. A statement was expected later it said.
Earlier, the independent Beta news agency said the army had returned to its barracks, signalling it would not interfere in the street protests.
Celebration
The demonstrations are the biggest show of strength yet by the opposition which says its candidate, Mr Kostunica, won an outright victory in presidential elections last month.
The BBC's World Affairs Editor, John Simpson, says there is a party atmosphere in the Yugoslav capital.
In an e-mail to BBC News Online, Belgrade resident Jelena Popovic wrote: "People are celebrating victory and no chaos at all."
Vijin Simic wrote: "The most amazing thing is that tear gas which was constantly thrown into the crowd, didn't scare away us and without a fear we stood in a front line."
In a speech to vast crowds on Thursday evening, Mr Kostunica said Serbia had been "liberated" from Mr Milosevic's rule, and that the Yugoslav president had fled his home.
Later, in an interview on state television he appealed for order and said there should be no political revenge.
Mr Kostunica said he was ready to normalise relations with the rest of the world - he said the French government had told him that sanctions against Serbia would be lifted as early as Monday.
But there were casualties on the day, reports said one girl had died and three others had suffered gunshot wounds. Up to 100 other people were reported to have been injured.
Levers of power
Serbian state TV went blank for several hours during the day, after demonstrators took over the building.
However it later began broadcasting again, with the message: "This is the new Radio Television Serbia broadcasting."
Later on Thursday, state-run news agency Tanjug, long seen as the mouthpiece of the Yugoslav leader, called Mr Kostunica the "elected president of Yugoslavia" and said it was now "with the people of its country".
Elsewhere in Serbia, demonstrators were reported to have broken into a state-run television station in the city of Leskovac.
'Path to democracy'
As the protests escalated, several world leaders urged Mr Milosevic to step down.
He later added that the US was ready to lift the economic sanctions imposed on Serbia and give people the help they deserved, once democratic forces were in control.
In Moscow, Russian President Vladimir Putin said he wanted to see an end to Yugoslavia's international isolation and for the country to develop along democratic lines.
"We are ready to contribute to this country overcoming the current crisis, coming out of international isolation and putting itself firmly on the path of democratic development," he said.
Russia has been a long-standing ally of Yugoslavia, notably during Nato's campaign of air strikes last year.
The President of the European Commission, Romano Prodi, said it was time for a peaceful transition to democracy in Serbia.
He said Mr Milosevic should now listen to his people, and leave the scene. Mr Prodi said that Europe would welcome the new Serbia.