The Fazal and Judi Dench-starrer bagged two nods in Best Costume Design, and Best Make-up and Hairstyling categories and the actor feels grateful for the recognition.
"And here's to the @TheAcademy for nominating us for Costume Design and Hairstyling and Make up at the 90th oscars this year. It's an absolute honour.
"And my heartiest congratulations to all the other nominees in all categories. Great year and great films to be rubbing shoulders with," he wrote on Twitter alongside stills from the Stephen Frears-directed movie.
The Pakistani-American actor-stand-up comic, who also stars in the biographical film, said the Oscar nomination is surreal feeling for him and he would "never get over" it.
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"Emily and I met when she heckled me at a comedy show in the back of a diner in 2006. We wrote a movie about it and 12 years later we're nominated for an Oscar..." he tweeted.
He also praised "The Shape of Water" for scoring the highest (13) nominations at this year's Oscars.
"Kobe Bryant and I have the same number of career Oscar nominations," Nanjiani quipped.
Veteran actor Anupam Kher, who also stars in "The Big Sick", took to social media saying he was proud to be a part of the film.
"Congratulations @emilyvgordon and @kumailn for the #OscarNominations for Best Original Screenplay for @TheBigSickMovie. So proud to be part of this gem of a film," he wrote.