New York Gov. Cathy Hatchul first announced the congestion charge two years ago, but it was delayed and revised after complaints from some commuters and businesses.
The new plan revives one scheme she suspended in June, saying there were “too many unintended consequences for New Yorkers.”
Most drivers will pay $9 once a day to enter the congestion zone during peak hours and $2.25 at other times.
Small trucks and non-commuter buses will pay $14.40 to enter Manhattan during rush hour, while large trucks and tour buses will pay $21.60.
The prosecution met with great opposition, including from taxi drivers’ associations.
But the most vocal opposition has come from Trump, a New York native who has vowed to end the scheme when he returns to office this month.
Local Republicans have already asked him to intervene.
Congressman Mike Lawler, who represents a suburban district north of New York, asked Trump in November to commit to “once and for all ending this absurd pricing grab.”
A judge on Friday rejected an attempt by officials in the neighboring state of New Jersey to block the scheme on the grounds of its environmental impact in nearby areas.
Last year, New York City was named the world’s most congested urban area for the second year in a row, according to INRIX, a traffic data analysis company.
In the first quarter of last year, vehicles in midtown Manhattan were traveling at 11 mph (17 km/h) during the morning rush hour, the report said.