The protesters hurled stones at the convoy as it left the palace of a traditional chief in Jalingo, the capital of the northeastern state of Taraba, where Jonathan had gone on a courtesy call before holding a rally as part of his re-election campaign.
Nigerians will vote for their next president February 14.
Several vehicles were damaged in the attack, according to witnesses.
"As soon the convoy left the palace of the emir of Muri, the crowd threw stones and broke the windscreens of several vehicles and dented others," said Jalingo resident Clement Moses.
The crowd, made up mostly of young men, was angry at the heavy military and police presence deployed for the presidential visit.
Armed soldiers and policemen blanketed the city and forced businesses to close.
"People were angry with the huge military deployment for the president, while Boko Haram continue(s) to run over towns and villages in neighboring Borno, Adamawa and Yobe states," said Bala Jika, another resident.
"They kept shouting that soldiers should deploy to Sambisa forest in Borno state and fight Boko Haram instead of coming to the city and harassing the people already traumatized by Boko Haram," Jika said.
Policemen fired tear gas to disperse the crowds. There were no immediate reports of injuries or arrests.
Jonathan has come under heavy criticism at home and abroad over his response to Boko Haram.
The group has terrorized northern Nigeria regularly since 2009, attacking police, schools, churches and civilians, and bombing government buildings.
The Islamist group has said its aim is to impose a stricter form of Sharia law across Nigeria, which is split between a majority Muslim north and a mostly Christian south.
It has sacked dozens of villages close to the border with Cameroon this month, slaughtering residents and abducting others.
Thursday was not the first time the president's convoy was attacked.
On January 20, his motorcade was stoned in the northern city of Katsina, where he was campaigning. Jonathan faces a formidable challenge from a opposition alliance.