The two geologists were seized from their hotel in the eastern village of Hombori near the border with Niger, in an assault bearing the hallmark of Al-Qaeda linked Islamist militants.
A Hombori municipality source said seven armed men entered the hotel at about 1am (0100 GMT) on Thursday and made off with their hostages to the north of the country, a hotbed of Al-Qaeda militants.
Later on French radio the Frenchmen's driver described the abduction.
"They (kidnappers) were armed to the teeth. They quickly attacked the guards and then they came towards me pointing their guns, their Kalashnikovs," the driver identified only as Mamadou told radio station Europe 1.
"They attacked me, then they broke down the door of the hotel to get inside" and seized the Frenchmen, he said.
In Paris, French foreign minister Alain Juppé confirmed that the men had been taken "in circumstances that were not yet clear".
The Frenchmen "had not bothered to alert the embassy or consulate" in Mali's capital Bamako to their presence, a French diplomatic source added.
The latest kidnap brings to six the number of French hostages in the Sahel area, with the group known as Al-Qaeda in the Islamic Maghreb (AQIM) still holding four nationals abducted in Niger in September 2010.
Northern Mali is home to a number of AQIM bases used to launch attacks and kidnappings in the Sahel region on the southern side of the Sahara that includes parts of Mali, Algeria, Niger and Mauritania.
The two geologists were employed by a cement works in the region owned by the Malian firm Mande Construction Immobiliere and funded by the World Bank, according to a diplomatic source.
They were seized a day after a former French military official involved in efforts to free the hostages in Niger was shot and wounded in the shoulder.
An Italian and two Spaniards kidnapped in Algeria in October are also believed to be held by AQIM, although the group has not claimed responsibility.
At a regional security meeting in Bamako this week, delegates complained that a lack of support by Algeria for military operations against AQIM was a serious setback to efforts to crack down on the group.
"We must recognise that up against a transnational enemy, which is well organized and disposes of enormous financial and material means, we need to develop further our capacity to carry out joint multinational operations," Mali's army chief General Gabriel Poudiougou said Monday.
Negotiations for the release of the four Frenchmen, who were among a total of seven people snatched by AQIM in the uranium mining town of Arlit in Niger, have been complicated by the fallout from the conflict in Libya.
Thursday's kidnapping came the same day as news that a French woman aid worker seized two days ago in Yemen's restive south had been released.
AQIM grew out of Algeria's Salafist Group for Preaching and Combat, which took part in a civil war there that has now ended. Since 2007, AQIM has launched a range of operations in the vast Sahel strip south of the Sahara.
Operating from their bases in northern Mali, the radical Islamists have carried out attacks on troops and civilians, kidnappings, particularly of Westerners, of whom several were executed.
AQIM is also engaged in trafficking of various kinds, including weapons and drugs.