President Jonathan, 53, easily won the Peoples Democratic Party primary election despite a challenge from ex-vice president Atiku Abubakar, who was backed by a group of prominent northern politicians.
With his low-key approach, a series of unexpected events have propelled him to the doorstep of what could be a historic victory in Africa's most populous nation if he wins the April 9 election.
Jonathan would be the first elected president from the Niger Delta, the country's main oil-producing region, as well as the first from outside the nation's three main ethnic groups: Yoruba, Hausa-Fulani and Igbo.
Some say his candidacy could lead to a doomsday scenario, while others argue that it represents progress.
An arrangement within the PDP, which has won every presidential vote since a return to civilian rule in 1999, has seen the party rotate its candidates between the mainly Muslim north and predominantly Christian south every second term.
Jonathan, a southern Christian from the Ijaw ethnic group, was thrust into the presidency in May following the death of his predecessor Umaru Yar'Adua, a northern Muslim who had not finished his first term.
For that reason, some argue another northerner should have been given the nomination.
They are concerned that Jonathan's candidacy will undo the careful compromise helping hold the country together.
However others say the move is a sign that Nigeria has begun moving away from politics based on ethnicity.
Either way, the politician from a family of canoe makers has come to represent something larger than his quiet personality suggests.
Jonathan has enjoyed an almost accidental rise to power since ditching his job with a government agency in 1998. The following year, he became deputy governor for the key southern oil-producing Bayelsa State.
In 2005, his boss was impeached over money laundering charges in Britain and Jonathan took over as governor. Yar'Adua, in need of a southerner to balance his ticket, picked Jonathan for vice president in 2007.
In one of the US diplomatic cables recently obtained by WikiLeaks, Jonathan purportedly acknowledges his inexperience during a meeting with the US ambassador while he served as acting president during Yar'Adua's illness.
He says he was chosen as vice president to represent the restive Niger Delta.
"I was not chosen to be vice president because I had good political experience," the cable quoted Jonathan as saying.
"I did not. There were a lot more qualified people around to be vice president, but that does not mean I am not my own man."