French warplanes have bombed suspected Islamist positions around both towns since France launched a military operation in Mali on January 11.
A column of French and Malian troops entered Diabaly, said an AFP news agency reporter with the soldiers.
France has sent some 2,000 troops to help Malian forces fight the militants.
It has called on West African countries to speed up the deployment of a regional force of more than 3,000.
An Islamist group in Nigeria has said it carried out an attack last week which killed two Nigerian troops as they prepared to deploy to Mali.
Ansaru said it targeted the troops because the Nigerian military was joining efforts to “demolish the Islamic empire of Mali”.
Nigeria has pledged to send 1,200 troops to Mali, with the first 50 deployed on Thursday.
Togolese and Senegalese soldiers make up the remaining 100 troops already in Bamako, AFP reports.
Mali’s Islamist fighters fled Diabaly, about 400 km (250 miles) from the capital, Bamako, on Friday.
On Monday, French soldiers from the 21st Marine Infantry Regiment as well as parachutists and Malian troops entered the town after reconnaissance flights by Gazelle helicopters, according to an AFP reporter who was with the soldiers.
They had set out at dawn from the nearby government-controlled town of Niono.
French Defence Minister Jean-Yves Le Drian said that Diabaly was now under the control of French and Malian troops, AFP reports.
The central town of Douentza, about 800 km (500 miles) from Bamako, had also been recaptured, he was quoted as saying.
Army commanders had earlier expressed fears that Islamists fleeing Diabaly had planted landmines.
On Sunday, Jean-Yves Le Drian said France was seeking “total reconquest” of northern Mali.
“We will not leave any pockets of resistance,” he told French television.
The Islamist groups currently control a vast area in the Sahara Desert, larger than France.
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