In a ruling that was issued late Wednesday, the court found General Gilbert Diendere "guilty of complicity in illegal arrest and aggravated abduction" and sentenced him to 20 years in prison and a fine of one million francs (1,500 euros). Prosecutors had asked for a seven-year sentence.
Diendere is serving a life term for his role in the assassination of president Thomas Sankara in a 1987 putsch that brought Compaore to power.
Another defendant, colonel Mamadou Bamba, who was accused of having decided which students to arrest, was sentenced to 10 years in prison and the same fine.
A third defendant, Sergeant Victor Magloire Yougbare who was accused of driving the vehicle to transport the body, was sentenced in absentia to 30 years in jail and a fine of five million francs. A warrant has been issued for his arrest.
The three elite members of former President Blaise Compaore's guard went on trial on Monday over the murder of a student who had led protests against their boss.
Boukary Dabo was kidnapped by armed men on May 19, 1990 and taken to the main camp run by a presidential security regiment in the west African country.
He was tortured to death there and buried at Po, 150 kilometres (90 miles) from the capital Ouagadougou.
Although investigations began in 2000, it was only after a popular uprising led to the fall of Compaore's regime that charges were finally brought in January 2017.
The same year, the authorities announced that Dabo's remains had been found in Po, site of a commando force center where Compaore guards were trained.
Burkina Faso is currently ruled by a junta under Lieutenant-Colonel Paul-Henri Sandaogo Damiba.
He took power in a January coup, ousting elected leader Roch Marc Christian Kabore, who failed to stem a jihadist insurgency.