Three other policemen were given one-year suspended sentences.
The Interior Ministry said at the time the Islamists had died during an attempted prison break after being suffocated by tear gas.
However, a legal source said the men had died from asphyxiation in the back of a crammed police van while they were being moved to a jail on the outskirts of Cairo.
The government has launched a widespread crackdown on the Brotherhood since the army toppled Islamist president Mohamed Mursi last July after mass protests against his rule.
The Islamist movement has accused the authorities of large-scale human rights abuses. The government has denied the allegations and declared the Brotherhood a terrorist group which poses a grave security threat to the most populous Arab nation.
Lieutenant Colonel Amr Farouk, deputy head of Heliopolis police station, was sentenced to 10 years in jail with labour and three other policemen were given one-year suspended sentences on charges of involuntary manslaughter and extreme negligence.
Security forces have killed hundreds of Muslim Brotherhood members in the streets, arrested thousands of others and put top leaders on trial since Field Marshal Abdel Fattah al-Sisi deposed the country's first freely elected government.