At least 3,073 party delegates gathered at the national convention cast their ballot - in compliance with the country's Electoral Act.
Two aspirants - a male and a female - who had earlier obtained nomination forms withdrew from the race - an action that is rather symbolic.
All powerful organs of the party have since September endorsed Jonathan for reelection.
The delegates merely voted yes or no to a question on whether or not Jonathan's endorsement should stand.
The president, following the endorsement, went thanked the party and formally adopted his incumbent vice president Namadi Sambo as his running mate.
This ended earlier speculations that Jonathan may be contemplating a new running mate.
The PDP convention, which began in Abuja on Wednesday, runs simultaneously with the presidential primaries and convention of the opposition All Progressives Congress (APC), which is still in session in the commercial city of Lagos.
Voting by at least 8,000 delegates attending the presidential primaries is still ongoing at the APC convention and the result is not expected until much later today.
At least five aspirants are seeking to be the opposition party's candidate with two of them - former military ruler Muhammadu Buhari and former vice president Atiku Abubakar - tipped as the frontrunners.
APC, the country's first major mega opposition party with a national spread, hopes to cash on the wobbling state of affairs in Africa's biggest economy, allegations of corruption and festering security crisis.
The Boko Haram insurgency - now in its fifth year - is the country's major security headache, claiming at least 13,000 lives since 2009.