That game like the finals themselves has been postponed due to the COVID-19 pandemic which up to Wednesday had claimed the lives of 463 Britons -- 22 of them in Scotland.
If Scotland were to beat Israel they would play the winners of Norway versus Serbia to secure a place at a major tournament for the first time since 1998.
Clarke thanked the fans for ensuring that the game at Hampden would have been a sell-out but added global events surpassed the importance of a football match.
"This is a difficult letter to write because, as a father and grandfather there are far greater considerations in life right now and far greater responsibilities on all of us," the 56-year-old wrote in a letter issued by the Scottish Football Association.
"At the same time, I feel it important to recognise and show appreciation for the effort you all had gone to in ensuring our match against Israel would have been a sell-out."
Clarke said that like all lovers of the sport in Scotland the lack of football in recent weeks had affected him but there was a greater goal to be achieved.
"The world has changed in recent weeks and months and football, rightly, has had to take a step back as our government and our wonderful, brave and selfless NHS staff step-up their efforts to tackle a far greater opponent," he said.
Sport across the United Kingdom has been suspended with strict limitations on when people are allowed to leave their homes to try and halt the spread of the virus.
The former West Brom and Kilmarnock manager called on the fans to observe instructions to stay indoors.
"That sense of togetherness, loyalty and commitment is needed in our lives now, more than ever before," added Clarke.