He scored 1,532 votes to defeat other candidates in the race, including the governor of the northwestern state of Sokoto, Aminu Tambuwal, and Nigeria's Senate President Bukola Saraki, the officials announced.
The reason for the meetings is due to the controversies that have trailed the party's governorship and senatorial primaries in some states such as Zamfara, Ondo, Kaduna and Ogun.
He also commended the role played by Rivers State Governor Nyesom Wike towards ensuring a successful convention of the PDP in Port Harcourt.
All eyes are now on the dozen candidates vying to be nominated to challenge him from the opposition Peoples Democratic Party (PDP), the former ruling party.
"I congratulate His Excellency, Atiku Abubakar, Waziri Adamawa, and by the grace of God and the votes of Nigerians, the next President of the Federal Republic of Nigeria".
A member of the Atiku campaign organisation, who does not want his name in print, said the major decider was the 11th hour support of the candidature of Atiku by former President Olusegun Obasanjo and other past generals.
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In his acceptance speech, Abubakar said he learnt a lot under Obasanjo when he served as his deputy from 1999 to 2007. It is not a one man's job, it is a collective responsibility and I am prepared to listen to you, to take your advice, consult with you, work with you and together, we'll succeed and after we succeed, we shall all be partners in that success.
Chairman of convention planning committee Ifeanyi Okowa, who is governor of the southern Delta state, said all 12 contenders were still in the running.
Abubaker defected again in May to PDP where he on Sunday clinched the ticket to tackle incumbent President Buhari in the 2019 presidential election. We always knew from day one that only one person will emerge, so today's event is not surprising.
While speaking on their manifestos, all the presidential aspirants of the Peoples Democratic Party (PDP) stated that their drive for the contest was the need to move the nation forward.
The poll asked, "Who is the best candidate for @OfficialPDPNig [PDP]?"
Both Saraki and Dogara had initially defected to the All Progressives Congress (APC) until their recent return to the PDP.