Director Alankrita Shrivastava was presented with the award by "Doctor Who" star David Tennant during the festival's Closing Gala.
The film, which stars Ratna Pathak Shah and Konkona Sensharma in key roles, revolves around the lives of four Indian women seeking more from life than docile domesticity.
"I am so deeply honoured that 'Lipstick Under My Burkha' has won the ScotRail Audience Award at the Glasgow Film Festival.
"Right now, when the film has been refused certification for exhibition in India because it is a women-centric film with a female point of view, I think the award could not have been more timely," Shrivastava said in a statement.
"The fact that the people of Glasgow have loved the film is an affirmation of the relevance of the film across cultures and nations. It is an affirmation of the fact that women's stories need to be told, through the female point of view. This award gives me hope. It gives me courage.
"It makes me believe that as women, we must continue to tell our stories, undeterred by those who want to silence us," the director added.