He made the announcement on his Facebook site, saying the decision had been taken “after wide and thorough consultations”.
Mr Jonathan, a southerner, became president in February after the death of Umaru Yar’Adua.
The governing party has previously said its candidate should be a northerner.
The president’s Facebook statement said he would make a formal declaration of his intention to stand for election on Saturday.
Officials in the presidency have confirmed that the Facebook entry was genuine.
While some observers were surprised that Mr Jonathan had used Facebook to announce his candidacy, he said in July that comments on his page had influenced him in overturning his ban on the national football team.
He announced the ban after the Super Eagles’ poor showing in the World Cup finals.
“People may scoff, but we take the interactions seriously, we track the [Facebook] feedback,” a presidential adviser told the Reuters news agency.
“It’s a small platform perhaps, but it offers the possibility of change.”
Only a small fraction of Nigeria’s 150 million people have access to computers, but numbers are growing fast.
The announcement came as one of Mr Jonathan’s main rivals for the governing People’s Democratic Party’s nomination, former military leader Gen Ibrahim Babangida, launched his campaign.
Source: BBC News – bbc.co.uk