Usenov signed his cabinet's resignation and handed over the powers to the leader of parliamentary opposition, ex-Foreign Minister Roza Otunbayeva, Interfax news agency reported from capital Bishkek.
Later in a statement Otunbayeva declared that the power in this of Central Asian republic has been assumed by the government of popular trust, RIA Novosti reported.
Since Tuesday's protests against President Bakiyev, the Opposition has captured administration in Talas, Chui, Naryn and Issyk-Kul regions in the north and west and are said to be in control of several districts in Osh region in the south loyal to Bakiyev.
President Kurmanbek Bakiyev has fled the country by air, while Prime Minister Usenov left by road for Almaty in neighbouring Kazakhstan with his security in several off-road vehicles, Moscow-based Kommersant FM radio has confirmed.
Bakiyev left the country in a special aircraft which took-off from Manas International Airport around 8 pm (IST) for an undisclosed destination.
Russian agencies have reported that Bakiyev's family home has been ransacked and looted in the absence of any security guards.
The riots erupted as the agitators alleged corruption in the administration and protested against the rise in power prices recently.
The Interior Minister Moldomusa Kongatiyev was beaten to death by the opposition protesters in the western town of Talas.
Prime Minister Daniyar Usenov declared a state of emergency in an effort to contain the riots.
However shortly after emergency was declared, agitators marched towards the Kyrgyz television centre, ransacked the building and forced to halt all programmes. They also looted the radio building and took the deputy prime minister Akylbek Zhaparov hostage.
Protesters raised slogans like "Bakiyev out!" and "We don't want this rotten power."
The US, which has an air base in Kyrgyzstan to aid NATO forces in neighbouring Afghanistan, also expressed "deep concern" about the situation in this former Soviet nation.
Meanwhile in Thailand the 'red shirts' seized a satellite TV station from police.
Reports The Daily Telegraph: "Thai security forces fired tear gas and water cannon at anti-government protesters yesterday as thousands invaded a satellite station demanding that the opposition television station be put back on air.
"The spasm of violence at the compound 35 miles north of Bangkok was the most serious confrontation in nearly a month of demonstrations designed to force the government of Abhisit Vejjajiva to quit and call fresh elections.
"Thousands of 'red shirt' demonstrators loyal to Thaksin Shinawatra, the ex-prime minister surrounded the Thaicom compound, which was eventually abandoned by the police.
"Protestors had scaled a moat guarded with razor wire to force open the front gates, a move that prompted the security forces to abandon their weapons, shields, and body armour which could be seen floating on the water.
"Last night the management of the company, Thaicom, agreed to put the 'red shirt' protesters' fiery People TV - or PTV - back on air after negotiating with their leaders despite a government ruling that it remain blocked.
"The government pulled the plug on PTV under the state of emergency decree saying that the channel that broadcasts rallies and propaganda speeches was putting out false information.
"The government has deployed 30,000 personnel across the capital Bangkok which has been the focus of the demonstrations where thousands of 'red shirts' have blocked roads and shut glitzy shopping malls since the weekend."
See www.vastminority.blogspot.com for video links