Meryl Streep, Cate Blanchett, Ethan Hawke and Amy Adams were among those paying their respects to an actor widely considered among the best of his generation.
The list of mourners also included Michelle Williams, Julianne Moore, Joaquin Phoenix, Louis CK, Mary Louise Parker, John Slattery, Jerry Stiller, Marisa Tomei, Spike Lee and the director Mike Nichols. Playwright David Bar Katz, who found Mr Hoffman's body, looked visibly upset as he arrived.
Mr Hoffman, 46, was found dead on Sunday of an apparent heroin overdose in his Manhattan apartment. He leaves behind his partner of 15 years, Mimi O'Donnell, and their three children. Ms O'Donnell was seen cradling their youngest child as she entered the church.
Police did not allow anyone to linger outside, and the media was penned away from mourners.
A larger memorial service is being planned for later this month. Last night family and close friends gathered for a private wake.
Mr Hoffman was nominated for Academy Awards four times: for Capote, The Master, Doubt, and Charlie Wilson's War.
He also received three Tony nominations for his work on Broadway, which included an acclaimed turn in 2012 as the weary and defeated Willy Loman in Death of a Salesman.
The theatre community mourned the actor on Wednesday with a candlelit vigil outside his beloved Labyrinth Theater Company and with Broadway's marquee lights turned off for a minute.
More tests are needed to determine what exactly killed Mr Hoffman, who was found with a syringe in his arm and what authorities said were dozens of packets of heroin in his apartment.
Post-mortem examination results were inconclusive, authorities said.
Mr Hoffman spoke candidly about past struggles with drug addiction. After 23 years sober,he reportedly checked himself into rehab for 10 days last year after relapsing in 2012.