The accusations, first reported past year by the New York Times and the New Yorker, gave rise to the #MeToo movement, in which hundreds of women have publicly accused powerful men in business, government and entertainment of sexual misconduct.
More than 70 women have accused Mr Weinstein of sexual misconduct although the charges relate to only two of them.
It's expected that Weinstein's bond will be set at $2 million, CNN reports. Weinstein surrendered his USA passport and agreed to wear a monitoring device that tracks his location, confining him to the states of NY and CT.
Other women who have publicly accused Weinstein of criminal sexual assaults include actress Rose McGowan, who said Weinstein raped her in 1997 in Utah; Sopranos actress Annabella Sciorra, who said he raped her in her NY apartment in 1992; and Norwegian actress Natassia Malthe, who said he attacked her in a London hotel room in 2008.
Until the scandal, Weinstein was among the most influential forces in American film.
One of the accusers pressing charges is Lucia Evans, who told the New Yorker that Weinstein forced her to perform oral sex on him in 2004.
"I hope this gives hope to victims and survivors everywhere, that we are one step closer to justice".
"I still have very guarded hopes", McGowan said. "I think the world could use that face being gone".
"Now comes the tough part".
A month ago, Bill Cosby was convicted of drugging and sexually assaulting a onetime friend, one of dozens of women who have accused the comedian and former TV star of sexual misconduct. Several actresses and models accused him of criminal sexual assaults, but numerous encounters happened too long ago for any prosecution.
Argento condemned Weinstein at the Cannes Film festival earlier this week. "Today is for you - and also for the young women who would surely have become his next victims.Justice" - Actress Mia Farrow, also the mother of investigative journalist Ronan Farrow who helped break Weinstein story, addressing Mira Sorvino on Twitter.
As Weinstein made his way to the precinct door, the disgraced movie producer had a pair of books tucked under his arm. "The arrest and ensuing charges are the result of a joint investigation between the NYPD and the Manhattan District Attorney's Office", the NYPD said.
First-degree rape and criminal sex act are class B felonies, while third-degree rape is a class E felony.
Former actress Lucia Evans, who said Weinstein forced her to perform oral sex on him in 2004, is thought to be one of the women whose cases triggered the NY charges.
The Manhattan district attorney's office and NY police have investigated Weinstein for months, coming under growing pressure from the Time's Up movement to bring the disgraced producer to justice.
"Even tonight, sitting among you, there are those who still have to be held accountable for their conduct against women", she said.