Reports say the violence cut across 13 states, leaving behind burning buildings, neighbors hiding in their homes and hundreds injured.
Heavy gunfire echoed through cities, as shouting crowds burned tires and threw stones at security forces.
Many were feared dead, though federal officials declined to offer any figures for fear of further stoking tensions.
While Christians and Muslims have shared the same soil in the nation for centuries, the election result showing the Christian president’s more than 10 million vote lead over Muslim candidate Muhammadu Buhari stoked popular resentment. It also spread accusations of rigging in a nation long accustomed to ballot box stuffing and violence.
“The damage is immense. A lot of buildings have been torched: houses, businesses and religious centres,” said Umar Mairiga of the Nigerian Red Cross. Mairiga said the Red Cross estimated more than 270 people had been wounded and another 15,000 had been displaced by the violence.
Nigeria has a long history of violent and rigged polls since it abandoned a revolving door of military rulers and embraced democracy 12 years ago.
Legislative elections earlier this month left a hotel ablaze, a politician dead and a polling station and a vote-counting center bombed
in the nation’s northeast.
However, observers largely said Saturday’s presidential election appeared to be fair, with fewer cases of ballot box thefts than previous polls.
Election chairman Attahiru Jega announced results Monday night that showed Jonathan won 22.4 million votes, compared to the 12.2 million votes of his nearest rival, the former military ruler Buhari.
Jonathan also received enough votes across Nigeria’s 36 states and capital to avoid triggering a runoff.
“I want to ensure you we have discharged our responsibility to the best of our ability on a nonpartisan, impartial basis and we have done our best to satisfy the aspirations of Nigerians for free, fair and credible elections,” Jega said.
The West African nation of 150 million people is divided between a Christian-dominated south and the Muslim north.
A dozen states across Nigeria’s north have Islamic Shariah law in place, though they remain under the control of secular state governments.
Thousands have been killed in religious violence in the past decade, but the roots of the sectarian conflict are often embedded in struggles for political and economic dominance.
Buhari’s party brought a formal complaint against the nation’s electoral commission even before the vote count ended, alleging massive rigging in Jonathan’s homeland of the Niger Delta.
The letter also alleged that the computer software used to tally results had been tampered with in northern states to favor the ruling People’s Democratic Party.
“What is being exhibited to the world is not collated from polling units but … a lot of manipulations,” the letter read.
Both Buhari’s party and the opposition party Action Congress of Nigeria refused to sign off on the results.