Jonathan, who assumed office last year after the death of President Umaru Yar'Adua, received more than half of the votes cast in a weekend election, beating his primary challenger Gen. Muhammadu Buhari by about 10 million votes.
"I welcome that this election appears to be the most credible since the end of military rule in 1999," said British Foreign Secretary William Hague in a statement. "I congratulate the people of Nigeria for exercising their democratic duties and I congratulate President Goodluck Jonathan on his election."
The International Committee of the Red Cross said there were "many dead" and about 16,000 displaced during rioting in northern Nigeria.
Jonathan imposed a curfew and called for calm after rioters protested against alleged vote rigging, the BBC reports.
Previous elections were wracked by violence and allegations of fraud. The period leading up to the weekend vote was relatively calm and election observers said the vote was free and fair.
"These elections were not completely peaceful but it is to the credit of the Nigerian people that they voted in spite of the violence," said Hague.