Emergency services spokesman Ashraf al-Qudra said four other people were seriously wounded in the attack on the house in Rafah.
He named those killed as Mohamed Ghanem, 25, Abdullah Akhras, 27, and Bashir Abdel Aal, 20, and said six tank shells were fired in the attack.
The remains of the three men arrived in pieces, he added.
The latest deaths brought the overall toll in 10 days of violence in and around Gaza to 230 Palestinians killed.
One Israeli has been killed in rocket fire by militants in Gaza, who have sent hundreds of missiles into the occupied lands during the conflict.
NJF/NJF