Malawi were due to play Uganda in Blantyre in a warm-up game ahead of qualifiers next month for both countries in the 2013 African Nations Cup preliminaries.
However, Uganda has been battling an outbreak of the virus which so far has killed at least 16 people.
In a statement, the Football Association of Malawi said: "We have cancelled the friendly on advice from the (Malawi) government following the escalation of the Ebola disease in Uganda."
Ugandan health officials said there had been no new cases since the start of August and 32 patients in isolation at a government hospital were responding well to treatment.
There is no cure for Ebola which is transmitted by body fluids such as saliva, sweat and blood, but doctors can treat symptoms including diarrhoea and vomiting.
Uganda are scheduled to travel to Zambia for an African Nations Cup qualifier on September 8.