The General Confederation of Portuguese Workers (CGTP), the country's biggest union alliance, called the strike to protest against reforms introduced by the centre-right government.
The strike led airlines calling off about 45 percent of the 1,500 flights scheduled at Portuguese airports on Wednesday, according to airport operator ANA.
Labour Minister Maria do Rosario Palma Ramalho acknowledged that between 38 and 45 percent of schools were closed but played down the extent of the strike.
"The vast majority of Portuguese workers are at work... In the private sector, participation in today's strike is absolutely marginal," she insisted.
Hospitals were disrupted but staff kept a legally required minimum service. All metro stations in the capital were closed but some buses ran. At Santa Apolonia railway station, in the city centre, display boards showed a long list of cancelled trains.
At a demonstration which drew hundreds in Lisbon, 30-year-old protester Rafael Medeiros told AFP that the strike was the signal the government and parliament need to slow down the reform".
"The time has come to bring down the labour code reform. What's on the table is very bad for workers," CGTP secretary general, Tiago Oliveira, said on Tuesday.
He said the plan would increase "job insecurity" and the "the deregulation of working hours".
Unions are incensed by the government's attempt to simplify firing procedures, extend the allowed length of fixed-term contracts and expand legal minimum services required during strikes.
Last December, unions organised the first general strike in Portugal in 12 years, also to protest against the reforms.
That movement was supported by the more moderate UGT trade union confederation, which did not join Wednesday's action.
Prime Minister Luis Montenegro's right-wing government, which argues that the changes are necessary to make the economy more productive, negotiated for months with employers' representatives and the UGT to try to reach an agreement. But the talks broke down.
The cabinet has submitted to parliament a slightly amended version of the reform unveiled last year. The minority government must now try to secure the backing of the Socialist opposition or the far right, both of which have already expressed strong reluctance.
