Now is the time for all parties across the region to de-escalate tensions," Mr Cleverly said on Friday.
He condemned the attacks on Israel from Gaza and southern Lebanon, and noted "Israel's right to self-defence".
He also criticised Israeli police for "violence" inside Jerusalem's Al Aqsa Mosque after officers attacked Palestinian worshippers inside Islam's third-holiest site on Wednesday and Thursday.
Tensions have soared between Israel and Palestinians during what is both the Jewish Passover and the Muslim holy month of Ramadan, with fears of further escalation in the coming days.
Mr Cleverly urged all parties to "respect the historic status quo arrangements at Jerusalem's holy sites and cease all provocative action".
"When Israeli security forces conduct operations, they must ensure they are proportionate and in accordance with international law," he said.
He added that Israel and the Palestinian Authority must "take steps to honour the commitments agreed" at regional peace summits in recent months attended by various parties, including Israeli and Palestinian officials.
"Peace will only be sustainable if both Israelis and Palestinians recommit themselves to a negotiated settlement, leading to a two-state solution of a secure Israel side by side with a viable Palestinian State," Mr Cleverly said.