West Ham midfielder Tomas Soucek and Roma's Patrik Schick missed Friday's 3-1 win over Slovakia after being forced to self-isolate after coming into contact with a staff member of the Czech team who tested positive for Covid-19 earlier this week.
"The national team will not play against Scotland on Monday due to representatives decision and the current situation with the Covid-19," said the English Twitter account of the Czech national team.
"The national team ends current preparations with the immediate effect straight after the win against Slovakia."
In a further statement, the Czech federation added: "There is great concern that the virus could spread further."
There was no immediate comment from the Scottish FA after Scotland's 1-1 draw against Israel at Hampden on Friday.