The friendly match was to have been played on June 9 in the Spanish coastal town of La Línea de la Concepción.
"I have signed the decision prohibiting the match from taking place," said Mayor Juan Franco, according to the AFP news agency.
Franco said the match was being stopped as a "precautionary measure" and that he was following recommendations from the regional health authority.
The Congo-Kinshasa national team had previously been forced to cancel its planned national team training camp at home due to the latest Ebola outbreak in the country.
The national team is now instead in Belgium, where it will face Denmark in a training match on Wednesday.
