Natasha, 26, is currently pursuing Masters in Business Management in Kolkata.
Loiloi from Manipur bagged the first runner-up position and Ragasya from Chennai was crowned the second runner-up.
The 16 finalists represented some of the Indian states.
They were chosen after a rigorous hunt involving more than 1,500 trans women across India.
"The winner will go to Thailand for Miss International Queen, the first runner-up will compete at Miss Transsexual Australia. We are looking for another international pageant so that we can send the second runner-up too," pageant organiser Reena Rai, founder and chairperson of Suhani Dream Catchers Pvt Ltd, had earlier told IANS.
Raveena also performed to the Lady Gaga track "Born this Way".
Transgender social activist Gauri Sawant, one of the jury members, said: "This is the first organized pageant on a national level for the transwomen after the Nalsa judgement so, I strongly believe that this is going to empower transsexuals and would aspire them to dream of winning the crown and representing their country and community on an international platform."
She was joined by former Mr Gay India Sushant Divgikar, fashion stylist Shaine Soni, educator and grooming expert Avleen Khokhar, nutrition and beauty expert Varun Katyal and Hector Ravinder Dutt, Principal of Delhi Public School Rohtak, among others, on the judging panel.