Riots broke out in Nigeria's predominantly Muslim north after Jonathan, from the mainly Christian south, emerged as the election winner, the BBC reported.
A civil rights group said the violence has killed more than 200 people while the Red Cross estimated that tens of thousands of Nigerians have fled their homes to escape it.
Parts of the Muslim north charged the elections were rigged and armed protesters took to the streets chanting the name of former military ruler Muhammadu Buhari, Jonathan's main opponent, CNN reported.
"We are shocked by these horrific acts, which strike at the heart of our nation," Jonathan said in a statement. "These acts of mayhem are sad reminders of the events that plunged our country into 30 months of an unfortunate civil war (in 1967)."
Jonathan said his government will use any "lawful" means necessary to restore the peace.