Former military ruler Muhammadu Buhari has become the first Nigerian to defeat a sitting president through the ballot box, putting him in charge of Africa's most populous nation and its biggest economy.

Al Jazeera's Yvonne Ndege, reporting from the capital Abuja, said the election commission made the official announcement after nearly all votes had been tallied.

"Buhari was able to get more than 25 percent of votes in 24 states, which means there won't be a run-off vote," she said.

To win the election, Buhari had needed to win more than 50 percent of the total votes nationally - and take at least 25 percent of the vote in two thirds of the states.

According to the Reuters news agency, Buhari's All Progressives Congress (APC) party won by 2.1 million votes, with 15.4 million votes versus 13.3 for Jonathan and the PDP.

The APC said their candidate received a phone call from incumbent President Goodluck Jonathan during which he immediately conceded defeat and congratulated Buhari on his victory.

"President Jonathan called General Muhammadu Buhari, the winner of the elections, to congratulate him," Lai Mohammed, spokesman for the APC, said.

"There had always been this fear that he might not want to concede, but he will remain a hero for this move. The tension will go down dramatically,

"Anyone who tries to foment trouble on the account that they have lost the election will be doing so purely on his own," he added.

Victory for Buhari marks the first time in Nigeria's history that an opposition party has democratically taken control of the country from the ruling party.

Al Jazeera's Haru Mutasa, reporting from Lagos, said there was shock that Jonathan had congratulated Buhari and that violence had not followed the announcement.

"The announcement has been greeted with celebrations across the country," Mutasa said. "Many people are excited and hope this will mark a new beginning and the country moves forward."

The 72-year-old built an early lead in northern states dominated by the mainly Muslim, Hausa-Fulani ethnic group of which he is a member.

Jonathan, whose five years in office have been plagued by corruption scandals and an insurgency by the Boko Haram group, was trailing by around 500,000 votes before votes in pro-opposition areas were counted.

In the previous election, more than 800 people were killed in protests after Buhari was defeated by Jonathan.

There was a brief protest by Jonathan's Peoples Democratic Party (PDP) before the counting had resumed on Tuesday.

Former Niger Delta minister Godsday Orubebe accused elections chief Attahiru Jega of being "partial" and "selective".

Orubebe claimed Jega had refused to investigate PDP complaints about big wins by Buhari in northern states but had launched a probe into claims by the APC of irregularities in Rivers.

"Nigeria has been reduced to a failed state." - What Muhammadu Buhari told Al Jazeera last month

Jega said later: "I don't believe that the allegations are substantial enough to require the cancellation or rescheduling of the elections in Rivers state. We will take the results."

International observers gave broadly positive reactions to the conduct of the vote, despite late delivery of election materials and technical glitches with new voter authentication devices.

Nigeria's Transition Monitoring Group, which had observers across the country, said: "These issues did not systematically disadvantage any candidate or party."

Al Jazeera