Modi resigned from the post before he took the oath of office as Prime Minister recently.
"Amit Shah, who was the vice-president of the GCA, was elected unopposed today as the president of the association," another GCA vice-president and Rajya Sabha MP Parimal Nathwani said.
"The name of Shah was proposed by me and he was elected unopposed," Nathwani said.
"The post had fallen vacant as former president of GCA Narendra Modi resigned (from the post) before he took oath as the Prime Minister of the country," he further said.
There are 32 members in the body of GCA.
Prime Minister Modi had taken over the reigns of GCA by replacing the then Congress leader Narhari Amin on September 15, 2009.
Amin later switched over to BJP. Shah, the former Gujarat Minister of State for Home and a close aide of Modi, was elected vice president of GCA in the same year.
With Shah as the BJP in-charge of Uttar Pradesh during the recent Lok Sabha elections, the party won 73 out of 80 parliamentary seats. Shah is currently vice-president of BJP.