The incident has been widely reported over past weeks in a country faced with increased cases of sexual harassment since its 2011 revolution.
The two policemen allegedly stopped a car driven by a man and demanded to escort his female passenger home.
Signup to our newsletter and follow us on Facebook and Twitter!
Instead, they drove her off in a police truck to an isolated area and tore off her clothes and sexually assaulted her, according to the charge sheet.
They face up to life in prison if convicted, a judicial official told AFP.
President Abdel Fattah al-Sisi has passed a law last June to combat sexual crimes and ordered police to crack down on harassment and cases of sexual assault.