The council's Development Management Subcommittee refused permission for development due to it being located within the St John's Road Pollution Zone.
The 21,000 sq ft store would have included a 140-capacity car park and brought thousands more vehicles to an area ranked as Scotland's most polluted street.
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Over 450 people had lodged objections to the plans.
Emilia Hanna, air pollution campaigner for Friends of the Earth Scotland, said: "We are delighted that Councillors have listened to local residents and their own officers and rejected this entirely inappropriate development.
"The supermarket and car park would have created more traffic congestion and air pollution and worsened people's health in Corstorphine. St John's Road is now Scotland's most polluted road, with levels almost twice the legal limit.
"This is an important result which will help communities all over Scotland oppose developments which would increase air pollution."
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