The warning was issued by Abu Obeida, spokesman of Hamas' armed wing al-Qassam Brigades, in a short text message, where he held Israel fully responsible for the continuing violations at the mosque.
"What happens at the Al-Aqsa Mosque, whether attacks, provocations or dangerous practices against worshippers, will be a cause for an explosion in the face of the occupation," Obeida said.
"Our patience won't last too long," he added.
On Saturday night, Palestinian militants fired three projectiles from the Gaza Strip into southern Israel, according to Palestinian and Israeli sources.
Israel Radio reported that two rockets were intercepted and a third one landed on an empty field, causing no injuries or damage.
No one claimed responsibility for the attack.