Riot police pushed the protesters back, beating their shields with truncheons and firing tear-gas grenades.
Kubatbek Baibolov, a senior member of For Reform, said: "Given the authorities' brutality we have to stop our protest for now."
Bakiyev has faced a string of protests since he won an election in 2005 after protesters stormed the government headquarters, prompting Akayev to flee to Russia.
Security forces accused the opposition of failing to control the crowd and arrested 35 people after the protests. Police were questioning senior opposition politicians, who earlier distanced themselves from Thursday night's disorder.
"The organisers have admitted they could not control the situation," Elmurza Satybaldyyev, a general prosecutor said. "We have launched a criminal case."
Kyrgyzstan's relative freedom to protest contrasts with other, more authoritarian Central Asian states.
The country, home to a US and Russian military airbase, has lurched through a series of political crises since former president Askar Akayev was deposed by violent protests in 2005.
Kanybek Imanaliyev, a member of the For Reform opposition movement, said police had seized on Friday editions of three main oppositions newspapers. There was no immediate police comment on the seizures.
Eight interior ministry troops were injured during Thursday's protests, as well as seven rioters, police said.
The RIA news agency quoted Isa Abdrakhmanov, an opposition leader, as saying that the violence on Thursday involved radicals and had nothing to do with the opposition.
He said: "We don't carry any responsibility for what is happening in front of the government building."