The 40-year-old woman, who works for Aga Khan Foundation as a senior technical adviser, was kidnapped outside her office in the heart of Kabul on June 9.
"I am happy to inform you that Judith D'Souza has been rescued," Swaraj tweeted.
She also thanked Afghan authorities for securing her release. "Thank you Afghanistan - for all your help and support in rescuing #Judith."
The External Affairs Ministry was in constant touch with Afghan authorities to ensure the safe release of Judith, who hails from Kolkata.
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It was not immediately known who were Judith's captors and how she was rescued. She was abducted along with two other persons.
The External Affairs Minister also lauded the efforts made by India's Ambassador to Afghanistan Manpreet Vohra in ensuring Judith's release.
In Kolkata, her family thanked the government for its efforts to secure her release.
"We are thankful to the Indian government for the rescue of our sister. We are now waiting for her to be back home. We would request the media to respect our privacy," Judith's sister Agnes told PTI.
In the letter, the family members had said that the "brave, thoughtful, generous and compassionate" Judith had been working in Afghanistan for the well-being of the Afghan people and "as an ambassador of goodwill from India's people".
During a meeting with Afghan President Ashraf Ghani on the sidelines of the annual summit of Shanghai Cooperation Organisation in Tashkent last month, Modi had requested the latter's intervention in securing Judith's release.