Wednesday's statement also urged all sides to work immediately to restore calm as tensions rise between Israelis and Palestinians.
Palestinian attackers on Tuesday burst into the crowded synagogue during morning prayers with meat cleavers and gunfire. It was the deadliest attack in Jerusalem since 2008.
Palestinians are angry over continued Israeli settlement building and a belief, despite official denials, that Israel is scheming to take over their most revered site.
The council statement condemns all acts of violence and notes that the tensions have affected both the Israeli and Palestinian people.