"I am shocked and deeply distraught on hearing that (the rape survivor) has passed away. In the brief time that I spent with (her), I was overwhelmed by her positive spirit, her sense of self, her dignity, her self respect, her humility, and her courage to stand up against all odds," the superstar tweeted on Friday.
The 40-year-old Anglo-Indian died on Friday following multiple organ failure while suffering from encephalitis.
She had appeared as a guest on Aamir's show "Satyamev Jayate".
"I was inspired by the love and humanity that she had in her heart. In her tragically short life she has given us a lot. I feel grateful that I could make her an acquaintance.
"Everyone who has had the good fortune of receiving her love and respect will miss her deeply. My thoughts are with her family. You will always be in our hearts. Love and respect," said Aamir, who turned 50 on Saturday.
Coming out of a night club in Park Street, the woman was allegedly raped at gunpoint inside a moving car in February 2012.
The mother of two revealed her identity in 2013 and marched on the streets of Kolkata to protest a series of rapes and murders in the state.
West Bengal Chief Minister Mamata Banerjee had courted controversy after she dubbed the incident as "fabricated".
Police subsequently cracked the case and arrested most of the attackers.
While five persons have been charged with the offence by a court, only three are behind bars. Two others, including the prime suspect, are on the run and remain untraced.