Instead, each soldier will serve a 10-year prison term.
"The death sentences by firing squad passed on 66 soldiers in January and March 2015 by separate general court martials have been commuted to 10 years imprisonment each," Colonel Sani Usman said in a statement.
The sentences were commuted following a review by the military authorities.
Usman said 71 soldiers were arraigned on several charges, including criminal conspiracy and conspiracy to commit mutiny.
"They were tried, discharged on some charges but found guilty and convicted on other charges -- which included mutiny," he said.
The military said in May that 579 officers and soldiers were facing two separate trials over indiscipline.
The 66 had been condemned to die by a military tribunal in two batches in September and December 2014, with their death sentences confirmed by a military council in January and March this year.
Under the regime of former president Goodluck Jonathan, Boko Haram captured swathes of territory in the restive northeast as Nigerian soldiers refused to deploy for operations and even fled before and during attacks.
Former national security adviser Sambo Dasuki and other high-profile suspects are currently facing trial for misappropriating billions of dollars meant to buy weapons to fight the insurgents.
Nigeria's military has been under pressure to end the six-year Boko Haram insurgency that has claimed at least 17,000 lives and forced some 2.6 million to flee their homes.
Buhari who took over in May, has given the military until the month's end to end the unrest.
Boko Haram which seeks to impose a hardline Islamic state in northern Nigeria has also carried out cross-border attacks in Chad, Niger and Cameroon.