Mix diatomaceous earth with enough water to make a paste of toothpaste-consistency. Roughly 1 pound of this mixture will cover 1 square foot of stain.
Spread a 1/2-inch layer of poultice over the rust stain and the inch of granite surrounding it. Press the layer down firmly to make sure it makes firm contact.
Cover the poultice with plastic wrap. Tape the edges of the plastic wrap down to create a seal.
Remove the plastic wrap after 24 hours.
Scrape the putty off with a plastic spatula once it dries.
Wash the spot with soapy water--one teaspoon per quart of water. Rinse with clean water and pat dry.
Observe the granite. If the rust stain isn't gone, re-apply the poultice. If the second poultice does not remove the stain, the Marble Institute of America advises that the stain is likely permanent.