Zuckerberg was accompanied by president-elect Joko Widodo during the visit to the Tanah Abang market in the heart of the capital where vendors take up road space, causing traffic congestion, local broadcaster TV One reported.
Star-struck traders and visitors tried to shake hands with Zuckerberg, who was wearing a business suit in a departure from his trademark hoodie and jeans.
Zuckerberg was in Indonesia to promote internet.org, a global partnership dedicated to making affordable internet access available to the world's poor.
Indonesia is one of the largest Facebooking countries, with about 70 million users of the social networking website, according the company.