The festival will take place from October 29 to November 5.
This is the second time an Indian film will do the honours of opening the festival after Govind Nihalani's "Hazaar Chaurasi Ki Maaa" in 1997.
"I am overjoyed that 'Aligarh', my first film about a city other than Mumbai is the opening film of the festival. This is a befitting reward for a team that has worked selflessly to make a film they are passionate about," Mehta said in a statement.
He added that the festival holds a very special place in his heart.
"We (Eros International, my team and me) are looking forward to the night and to sharing this special film with the amazing MAMI audience," he said.
According to festival director Anupama Chopra, "Aligarh is a powerful film that tells an important story on a sensitive subject. Our mission is to showcase exciting and thought-provoking stories and I am sure our audience will enjoy our festival opener."
Set in a town in Uttar Pradesh from which the film takes its name, "Aligarh" is the story of a professor (Manoj Bajpayee) fired for his sexuality and a young journalist (Rajkummar Rao) who tells his story to the world.
The film will also be screened at the ongoing 20th Busan International Film Festival and later this month at 59th BFI London Film Festival.