More than two-thirds of Nigeria's 36 states have declared returns in the vote pitting Jonathan against former military ruler Buhari in the closest election ever in Africa's most populous country and biggest economy.
Buhari held a lead of roughly 500,000 thousands votes but appeared to be in a strong position with a number of pro-opposition areas yet to report.
Results are still pending from the northeast states hit hardest by Boko Haram -- Borno and Yobe -- which are expected to overwhelmingly back Buhari.
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.
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He is likely to gain further ground when a group of states in the northwest deliver returns.
Jonathan has so far won near total support in the southern, oil-producing Niger Delta, taking 98.4 per cent in his home state of Bayelsa and 94.9 per cent in neighbouring Rivers, where results were disputed by the opposition.
There was a brief protest by Jonathan's Peoples Democratic Party (PDP) before the count resumed, with former Niger Delta minister Godsday Orubebe accusing 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 Buhari's All Progressives Congress (APC) of irregularities in Rivers.
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."
In Kano, the 72-year-old defeated Jonathan by nearly 1.7 million votes after besting the president by roughly one million in 2011.
And in Kaduna, where the two ran neck-and-neck in 2011, Buhari won by 650,000 votes.