A few dozen masked protesters dressed in black threw rocks and other objects at police as anti-police slogans echoed through the streets and anti-police graffiti covered nearby walls.
Firefighters extinguished several fires, including on buses, while police responded with tear gas, according to Reuters witnesses.
The clashes occurred as thousands of protesters took to the streets of the Belgian capital including students inspired in part by demonstrations in neighbouring France.
The strike disrupted public transport and air travel while many schools and childcare facilities were also affected.
Among the demonstrators, some carried placards reading "I skipped class to defend class" and "Education is a right, not a privilege".
The Belgian walkout is part of a wave of protests sweeping Europe, with students in France and Italy, among other countries, taking to the streets over education funding while tens of thousands have rallied in Spain over a housing crisis.
Police said while the march itself - joined by about 30,000 people - passed off peacefully, clashes erupted near Brussels Central Station where groups threw bottles, bricks, stones and fireworks at police, set rental bikes on fire and damaged public property.
Police said officers used water cannon and tear gas to disperse the groups and that 21 people had been detained or arrested, including 13 minors.
The strike was called by Belgium's two largest unions, the socialist FGTB/ABVV and Christian CSC/ACV, which oppose government budget measures they say would make workers, pensioners and low-income households bear the burden of efforts to reduce the country's deficit.
Ahead of the march, FGTB/ABVV president Bert Engelaar urged rioters to stay away from the protest.
"Those individuals have nothing to do with the message with which thousands of others come out on the streets," Engelaar wrote on Facebook.
Belgian Prime Minister Bart De Wever said on Thursday that painful budget measures were needed now to avert a looming debt and interest-cost spiral that would otherwise leave future generations with a heavy bill.
Student groups, whose protests began earlier this month in Liege and spread to Brussels on Friday, say they are also protesting rising education costs, overcrowded classrooms and reforms they fear will make higher education less accessible.
"We're not taken into account at all and no one seems to realise that it's hard for us too, both for workers and for students," said Emilie L'Honneux, a 23-year-old student from Liege.
"We're struggling too, and we are the future of this country," she added.
with DPA
