The prosecutors office said Uber's global CEO Travis Kalanick and a local rental car service operator were indicted for violating a law governing passenger transport services.
Both were not detained, and it was not immediately clear whether Kalanick would visit Seoul for trial.
In South Korea, rental car service operators are banned from conducting passenger transport business using their cars. Violators face up to two years in jail or a fine of 20 million KRW ($18,150, roughly Rs. 11 lakhs).
The Seoul city government has filed complaints with prosecutors, saying Uber's operations raised passenger safety issues and threatened the livelihood of licensed taxi drivers.
City regulators have launched a crackdown on drivers and rental cars that cooperate with Uber. A financial reward of up to one million won was offered for those who report Uber's activities.
California-based Uber is the most prominent of several smartphone apps that are shaking up the traditional taxi landscape in cities around the world.
It has already faced significant resistance from regulators in several countries, who accuse it of unfair competition and lacking in standards.
Uber has also sparked angry protests by cab drivers in France and other countries who fear it is chipping away at their client base.
It made headlines this month when an Uber driver allegedly raped a passenger in New Delhi.