The militant attack on a police base in the north of the country also left one police officer dead and seven officers injured, police said.
The army says 24 fighters were killed in the first operation on Friday and a further eight in a second on Saturday, in the north of the country.
It was the third deadly attack suffered by the Canadian firm Semafo in 15 months in the West African country, which is battling growing violence.
The village of Zoura lies in Bam, one of a swathe of provinces in northern Burkina Faso that have been battling with a four-year-old wave of militant violence that came from neighbouring Mali.
Armed men attacked the Grand Mosque in Salmossi on Friday evening - 13 died on the spot and three succumbed to their injuries later.
There has been speculation talk of a military coup in the African country after recent attacks left dozens of soldiers dead near the border with Burkina Faso.
Meanwhile, France has begun asking its European partners to send special forces to Mali and other Sahel nations in Africa, to shore up local forces who are being increasingly targeted by deadly militant attacks across the vast desert expanse.
The armed attack happened in the village of Komsilga, in the Zimtanga district, two weeks after similar attacks killed nine civilians in the same region.
The West African country has been battling with a rising wave of violence since 2015 which left at least 500 dead.
Malian authorities revised the death toll down to 35 from a previous estimate of 95. On Monday, a militant group massacred villagers from the Dogon ethnic group in southern Mali.
"Several dozen armed men carried out an attack on the district of Arbinda, shooting several people dead," a local official tells AFP news agency.
Officials say gunmen set fire to the church, several shops and a small cafe after killing at least six congregants including a priest during mass in a Catholic church in Dablo, northern Burkina Faso.
Subscribe to our Youtube channel for all latest in-depth, on the ground reporting from around the world.
Copyright © 2019 TRT World.