Palestinian militant group Hamas launched a series of attacks on the country, killing hundreds and taking up to 150 people hostage.
Ceferin made his remarks on behalf of the European football community in a letter sent to the chairman of the Israel Football Association.
Israel's Euro 2024 qualifier against Kosovo on Sunday has been postponed.
Israeli authorities will not allow the national team to travel abroad, and a new date for the fixture will be announced in due course.
In response to the attacks by Hamas, Israel has launched air strikes on Gaza and prevented the passage of food, water, fuel and medicine into the territory.
"On behalf of Uefa and the European football community, I am writing to express our profound sorrow upon learning about the tragic acts of violence that occurred last week in Israel, resulting in the loss of innocent lives," said Ceferin in his letter.
"My heart goes out to all the victims and their families during these difficult times. It is an unimaginable tragedy, and the pain and sorrow are profound and resonate across the entire football community.
"We sincerely hope no one will ever again experience such grief.
"My friend, I pray for these deep wounds to heal and for a world where such senseless acts of violence have no place."
Players Will wear black armbands during Friday's match between England and Australia and a period of silence will be held in order to respect "the innocent victims of the devastating events in Israel and Palestine".
The UK government had written a letter encouraging governing bodies in sport to "appropriately" mark the attacks in Israel this week with shows of support for the victims.
The Premier League, English Football League and Women's Super League all issued statements on Thursday expressing shock and sympathy at the events, and announcing plans to wear black armbands at upcoming matches.
