On Wednesday, riot police entered Malandrino, cutting off access to the roof.
The authorities asked the inmates, who spent a cold and rainy night on the roof, to return to their cells.
Protests had died down in prisons in Athens, on the Ionian island of Corfu, the Aegean island of Crete, the central towns of Larissa and Trikala, the western city of Patras, the northern city of Salonika and the northeastern town of Komotini by the end of Tuesday.
Three inmates were injured in a police operation in the high security prison of Korydallos in Athens.
Police use of tear gas led to complaints from the local authorities as the prison lies in in a densely populated area of the city.
Four Korydallos prison guards were hospitalised with breathing problems.
Prisoners in Malandrino have also made a series of demands for reduced sentences and longer leave but this was rejected by the Greek justice ministry.
The alleged beating of the inmate, a self-styled anarchist, was followed by a series of incidents in Athens believed to be staged in his support.
On Wednesday, a group of suspected anarchists threw stones and firebombs at the private offices of the Anastassis Papaligouras, the justice minister and George Voulgarakis the culture minister, formerly minister of public order.
Earlier on Thursday, another group threw firebombs at the headquarters of the Athens riot police department near the city centre.