Boni is home to several thousand people and was seized by unidentified jihadists yesterday afternoon until the early hours of today.
The militants fired on administrative buildings and set fire to the mayor's office, leading the army to recall its troops from the vicinity.
"The jihadists left Boni in the night and today around 8am the Malian army came back to take control of the town," a Malian security source told AFP.
Meanwhile an administrative source in the town said the jihadists "kidnapped a Boni community official" accused of giving information to the security forces by phone.
Ongoing international military intervention since January 2013 has driven Islamist fighters away from major urban centres which they had briefly controlled, but large tracts of Mali are still not controlled by domestic or foreign troops.
Jihadist groups early last year began to carry out attacks in central Mali as well as the long-troubled north.