Dozens of youths occupied the Senate for eight hours to demand a referendum on how to resolve Chile's social problems.
The activists left after getting a promise from opposition legislators that they will introduce a bill requiring a binding referendum, although political leaders on both right and left have said Congress itself must decide the dispute.
The occupation of the Senate headquarters in Santiago came just hours after riot police evicted protesters from galleries at the Congress building in Chile's port city of Valparaiso.
University and secondary school students have been boycotting classes and mounting demonstrations for nearly six months pushing their demand that the government make extensive changes in Chile's education system, including making public schools free for everyone.
The action at the Senate building began when students and other protesters flooded into a hearing room where the Senate's education budget subcommittee was meeting.
Three youths climbed atop the committee table and unfurled a sign reading "Plebiscite now" as education minister Felipe Bulnes and others at the hearing hurriedly left. Activists shouted at Mr Bulnes, who stumbled during scuffling on the way out. A young man broke a window and threw coins at the minister.
The protesters then occupied the Senate headquarters and transmitted the situation live over the internet by webcam. They urged other students to converge on the building, which housed Chile's congress before the 1973-90 military dictatorship.
Police sealed off the building with metal barriers to keep more people from entering and faced off with a crowd of about 600 protesters holding signs demanding "free education" and "referendum now." A few dozen activists tried to force their way in but were driven back by water cannons.
Senate president Guido Girardi, a member of the opposition, promised the protesters holding the Senate building that they would not be dislodged by force as were those at the Congress.
His promise drew criticism from pro-government legislators, including Senator Alberto Espina, who accused Mr Girardi of "a serious dereliction of duty" in failing to ensure the security of the hearing.
The protesters finally agreed to leave the building after talking with opposition senators and representatives who agreed to introduce legislation for holding a referendum.
The youths were put in police vehicles outside to have their identities checked. Interior minister Rodrigo Hinzpeter said they could face charges of threatening a minister of state and interfering with legislative work.
Students have been pressing for a national vote because they don't trust Chile's establishment, and the protests have won sympathy for the students from about 80 per cent of the population, according to opinion polls. At the same time, president Sebastian Pinera's support has dropped to between 20 per cent and 30 per cent.
However, Chile's constitution allows referendums in only very limited circumstances, such as when Congress and the president cannot resolve their differences.
Students are demanding the government provide free public education for all Chilean students, not just the poorest, and improve the quality of schooling. They also want state subsidies for private colleges reduced.
Mr Pinera's government has said it cannot afford to make education free for everyone, and student leaders have broken off negotiations with the administration.
The president has sent his own proposals for education changes to Congress, and appointed a commission of experts to provide him with further ideas in January.
AP