The government hopes lifting costly fuel subsidies, causing prices to rise by up to two thirds at the pumps, will help alleviate the worst crisis in decades in Africa's biggest economy.
A wave of strikes ensued the last time Nigeria tried to introduce a similar measure in 2012, and authorities eventually reinstated some subsidies.
This time around the Nigerian Industrial Court blocked industrial action due to the risk of civil disorder, but late on Tuesday the Nigeria Labour Congress (NLC) said it would go ahead with its planned indefinite strike anyway, starting on Wednesday.
"The government was not ready to accede to our demands, so we walked out of the meeting," Chris Uyot, deputy general secretary of the Nigerian Labour Congress (NLC), told Reuters.
A second union, the Trade Union Congress (TUC), abandoned its strike plans in response to the court ruling.
Reuters witnessed government offices, shops and banks in the capital Abuja mostly opening as normal on Wednesday.
Some 300 union activists gathered there to stage a march, and some 200 protested in the commercial capital Lagos, where some banks and many shops were also doing business.
'LEFT WITH NO CHOICE'
A fall in oil prices has eaten into the foreign reserves of Nigeria, which relies on crude sales for around 70 percent of national income. The central bank has adopted a fixed exchange rate to protect further depletion of reserves.
On Tuesday, vice president Yemi Osinbajo said President Muhammadu Buhari had been "left with no choice" but to raise petrol prices.
"What can we do if we don't have foreign currency? We have to import fuel," Osinbajo said.
Nigeria needs to import almost all of its fuel as its refineries are largely out of action after years of neglect and mismanagement.
There were some flight delays on Wednesday as airlines struggled to get jet fuel, but airports in Lagos, Abuja and Port Harcourt in the oil-producing Niger Delta were operational