A detachment in Foutouri, in the eastern province of Komandjari, came under attack at around 5 am, the army said in a statement.
"The vigorous response neutralised at least three assailants and led to the seizure of weapons and ammunition," it said, adding that two troops were treated for "light wounds" and then evacuated.
On Wednesday, 38 people were killed and 63 injured when rebels in eastern Burkina ambushed a convoy carrying employees of a Canadian mining company.
It was the biggest one-day death toll in the history of a nearly five-year-old militant insurgency which spread to the fragile Sahel state from neighbouring Mali.
Nearly 700 people have died, according to an AFP toll, and around half a million people have fled their homes, according to UN figures.