Results published in Abuja showed Jonathan surpassed his main People's Democratic challenger, former Vice President Atiku Abubakar, by a margin of 2,736 votes to 805, the BBC reported.
There were allegations of voting fraud in the Western African country that ended military rule in 1999, the report said.
Nigeria has a history of alternating elected leaders from the north and south, largely divided by Muslims in the north and Christians in the south, but the primary results broke with that tradition, the broadcaster said.
Jonathan, who had been vice president, became Nigeria's leader after the death of President Umaru Yar'Adua last May.
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