Fethi Dorduncu visited the house in the Greek city of Thessaloniki in May and wrote in the visitors' book that Erdogan was a "traitor" bent on destroying Ataturk's secular republic and building an Islamic state in Turkey.
Erdogan ripped the page from the book when he later visited the house, which is now a museum, in the city where Ataturk was born in 1881 when it was still part of the Ottoman Empire ruled from Istanbul.
The Ankara court ordered Dorduncu, who is in his 80s, to pay damages for the pain and anguish he caused Erdogan, the state Anatolian news agency said.
Erdogan's lawyers had originally sought damages of 20,000 lira.
Turkish secularists accuse Erdogan and his AK party of trying to dismantle Ataturk's secular state, founded in 1923 on the ashes of the old religion-based Ottoman empire.
Erdogan has filed a number of lawsuits against his critics, including journalists and cartoonists, sparking criticism from the EU that he is harming freedom of expression in Turkey.
Last week, a British artist was detained after painting a picture of Erdogan as a dog.