A government spokesman said the men's bodies were found in the open desert and their throats had been cut.
They were found about 30 km (20 miles) north of the town of Tourine - the site of the ambush.
The west Saharan Islamic state pleaded for international help in battling its growing al-Qaeda presence.
Three days of national mourning for the dead have been declared from Sunday.
Mauritania, which became a modest oil producer in 2006, says the Islamic Maghreb branch of al-Qaeda is a growing problem in the region.
Al-Qaeda's North Africa wing, which is considered active in neighbouring Algeria, had claimed responsibility for the ambush and said it was holding the soldiers.
The government initially reported that the soldiers had been shot dead in the ambush, but later said they believed they had been abducted.
The group had threatened action after a coup in August that toppled Mauritania's first democratically elected president.
Despite concerns over the growing terrorist threat in the country, the US suspended more than $20m (£11m) in non-humanitarian aid in protest over the coup.
A member of the country's Higher State Council, Colonel Ahmed Bemba Ould Baya, said the latest attack showed the country needed international help to fight extremism.
"This tragic episode puts the international community face to face with its responsibilities," he said.
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