The screenplay of the gay romance movie, directed by Luca Guadagnino, is based on the eponymous novel by Andre Aciman.
Ivory beat other movies contenders for "The Disaster Artist", "Logan", "Molly's Game" and "Mudbound" for the award.
This was Ivory's fourth Oscar nomination, but the first in the adapted screenplay ategory.
Earlier, Ivory had received directing nominations for "A Room with a View" (1986), "Howards End" (1992) and "The Remains of the Day" (1993).
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Ivory, flaunting a shirt emblazoned with the face of "Call Me By Your Name" star Timothee Chalamet, on Sunday night thanked his deceased Merchant Ivory partners Ismail Merchant and Ruth Prawer Jhabvala as well as Aciman.
"I wouldn't be standing up here without the inspired help I received from my life's partners, who are gone," he said. He continued, giving his "profound thanks to the members of the Academy", and giving a nod to Sony Pictures Classics.
Ivory and his partners collaborated on multiple films. Some, like "The Householder", "Shakespeare Wallah", "The Guru", "Bombay Talkie" and "In Custody", featured Bollywood star Shashi Kapoor, who died in December last year.
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