The bomber was killed before he could detonate his bomb on Saturday evening.
This was followed by militant attempts to infiltrate the city.
The army, backed by French air power, then moved against the Islamists.
Earlier this year French troops pushed Islamists out of much of northern Mali but sporadic fighting has continued.
“The fighting is heavy and it is ongoing,” Malian army Capt. Modibo Naman Traore told the Reuters news agency, adding that the army was in the process of “encircling” the militants.
At least one Malian soldier and two civilians were wounded in Saturday’s fighting according to the city’s mayor.
The number of casualties following Sunday’s fighting remains unknown.
The people of Timbuktu had barricaded themselves in their homes after a group of Islamists infiltrated a western neighborhood of the city overnight.
The French left the Malian army on the front line for hours before they intervened and finished the job.
Several residents reported a French jet firing on rebel positions.
Another militant attack on the northern town of Gao was repelled on Monday.
Islamist rebels seized much of northern Mali a year ago after a military coup in the capital Bamako.
France intervened militarily in January amid fears that the militants were preparing to advance on Bamako. It currently has about 4,000 troops in Mali.
Since the intervention began, major cities including Gao, Kidal and Timbuktu have been recaptured but fighting is still continuing in desert mountains.
Malian army and troops from several African countries, including 2,000 from Chad, have also been involved in the fighting.
France plans to withdraw its troops from Mali in April, with West African countries expected to take over in the run-up to elections due in July.
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