Military sources said on Sunday that 25 mortar shells had been fired at Jewish settlements, causing damage to three houses but no injuries.
Hamas, Islamic Jihad, the al-Aqsa Martyrs Brigades, Ahmad Abu al-Rish Brigades and the Democratic Front for the Liberation of Palestine all have confirmed they had shelled settlements in Gaza Strip in retaliation for the Israeli "crime".
Sami Abu Zuhri, a spokesman for Hamas, reaffirmed the right of "our people and its armed groups to respond to this dangerous aggression".
The killing of the three youths on Saturday was the deadliest incident in the territory since the main Palestinian resistance groups agreed to a de facto truce in January.
A spokesman for the Palestinian Interior Ministry, Tawfiq Abu Khusa, told Aljazeera that investigations revealed the three Palestinian teenagers were playing football when they were shot and killed.
Israelis earlier said the three were killed in a closed military zone after warning shots were fired, but an official later apologised over the incident.
According to Palestinian sources, Israeli Defence Minister Shaul Mofaz telephoned Palestinian Authority (PA) Interior Minister Nasr Yusuf on Saturday night to apologise for the incident.
Mofaz reportedly urged Yusuf to make sure the killings remain a "localised incident" and to not let them wreck the uneasy calm in the occupied territories.