Both suspects are Malian nationals from the country's unrest-wracked north, controlled by Tuareg-led rebels and jihadist groups linked to Al-Qaeda in 2012.
"In two separate operations in Bamako on Thursday, Malian special intelligence operatives arrested two jihadists who were preparing to commit a large scale attack in Bamako against foreign targets," a security official told AFP on condition of anonymity.
The attack was planned for the France-Africa summit on January 13 and 14, which gathered some 30 African states and France to discuss the fight against extremists, the struggle to improve governance and the migrant crisis.
But stringent security measures forced the suspects to delay their plans, the official said. Another Malian security source confirmed the report.
Both suspects are Malian nationals from the country's unrest-wracked north, which fell under the control of Tuareg-led rebels and jihadist groups linked to Al-Qaeda in 2012.
The Islamists sidelined the rebels to take sole control.
Although they were largely ousted by a French-led military operation in January 2013, implementation of a peace accord struck in 2015 has been piecemeal with insurgents still active across large parts of the region.
The suspects were arrested carrying "compromising materials," the official said, including a "GPS system, ammunition and explosive material."
"The first (suspect) was the logistics specialist who did the tracking," while the second was likely the would-be suicide bomber, the second security source said.
He also said that both men belonged to the group of Algerian jihadist and Al-Qaeda ally Mokhtar Belmokhtar, which claimed responsibility for a January 18 suicide bombing that killed more than 70 people in the northern city of Gao.
The group, allied to Al-Qaeda in the Islamic Maghreb (AQIM), targeted militia groups committed to restoring peace in Mali.
That attack, which struck a fresh blow at efforts to stabilise the troubled north, occurred five days after French President Francois Hollande visited the military base at Gao en route to the France-Africa summit.
French special forces had arrested several people ahead of the summit suspected of planning attacks during the gathering, according to Malian and foreign officials.