The industrial action follows a controversial government decision to end fuel subsidies from 1 January which has seen fuel prices more than double in Africa’s largest oil producer.
At least 10 people are reported to have been injured when protestors attacked a mosque in the city.
An appeal by President Goodluck Jonathan on national television on Saturday to win support for the government move was rejected by the unions.
Promise Adewusi, Deputy President of Nigeria Labour Congress, said the strike was the result of bad governance and the action would continue until there was a reversal of the pump price increase.
“It's been totally, totally successful. Nigerians have never witnessed a thing like it in the culture and history of their struggles,” he told RFI . “Everything is down, completely. It's an indefinite strike, we don't know how long this will last.”
There was massive security in the capital Abuja after protests last week became increasingly volatile with police firing tear gas and accused of using excessive force.
Security forces are already under pressure over violence blamed on Islamist Group Boko Haram.
Recent deadly attacks on Christians have sparked fears of a wider religious conflict in a country which is roughly divided between a mainly Muslim north and a Christian south.
The government says it spent more than six billion euros on subsidies in 2011 and President Jonathan says everyone must be prepared to make sacrifices to save the country.
But Nigerians view the subsidies as their only benefit from the nations’s oil wealth and are mistrustful of the government after years of corruption.