No one claimed responsibility for the rocket fire.
Following the incident, Ehud Barak, the Israeli defence minister, ordered that the crossings be closed indefinitely.
The move effectively seals off the Gaza Strip which badly needs supplies for its 1.5 million Palestinians.
Hamas denounced the Israeli reaction as an act of "sabotage" against the truce.
Khaled al-Batsh, a leader of the Islamic Jihad, also denounced the closure of the crossings.
He told Al Jazeera the Israeli move was expected and criticised Israel for not observing its part of the ceasefire deal.
"It is a normal, expected action by Israel which disregards its truce commitments - lifting the siege, opening border crossings and halting aggression. None of these conditions have been implemented," he said.