The woman, identified only as Gulnaz for her own protection, was at a women's shelter in Kabul Wednesday with her daughter, her attacker's child who was born in prison, CNN reported.
Afraid of reprisals, she had hid the fact of the attack by a cousin's husband and her resulting pregnancy as long as she could, but was eventually prosecuted and found guilty of sex outside of marriage -- adultery -- and sentenced to 12 years in jail.
She was just 19 at the time, and her case garnered international attention.
After Afghan Justice Minister Habibullah Ghaleb and a judiciary committee both proposed a pardon, Karzai ordered Gulnaz's release.
She could still be at risk in conservative Afghan society, as women in her situation are sometimes killed for the shame they are seen to have brought to the community, CNN said.