The toll, known as congestion pricing, is meant to reduce traffic gridlock in the densely packed city while also raising money to help fix its ailing public transit infrastructure.
Drivers of most passenger cars will pay $US9 ($A14) to enter Manhattan south of Central Park on weekdays between 5am and 9pm and on weekends between 9am and 9pm. During off hours, the toll will be $US2.25 for most vehicles.
After years of studies, delays and a last-ditch bid by New Jersey to halt the toll, the program launched without major hiccups early on Sunday.
Congestion Relief Zone tolling is now in effect. — MTA (@MTA) Learn more: https://t.co/AmEYRNH6IbJanuary 5, 2025
But transit officials cautioned the first-in-the-nation scheme could require adjustments - and likely would not get its first true test until the workweek.
"This is a toll system that has never been tried before in terms of complexity," Metropolitan Transportation Authority chair and CEO Janno Lieber said on Sunday.
"We don't expect New Yorkers to overnight change their behaviour. Everybody's going to have to adjust to this."
The fee - which varies for motorcyclists, truck drivers and ride-share apps - will be collected by electronic toll collection systems at over 100 detection sites now scattered across the lower half of Manhattan.
It comes on top of tolls drivers pay for crossing various bridges and tunnels to get to the city in the first place.
On Sunday morning, hours after the toll went live, traffic moved briskly along the northern edge of the congestion zone.
Many motorists appeared unaware that the newly activated cameras, set along the arm of a steel gantry above the street, would soon send a new charge to their E-Z Passes.
Some local residents and transit riders said they were hopeful the program would lessen the bottlenecks and frequent honking in their neighbourhoods.
President-elect Donald Trump, a Republican, has vowed to kill the program when he takes office, but it's unclear if he will follow through. The plan had stalled during his first term while it waited on a federal environmental review.
In November, Trump, whose namesake Trump Tower is in the toll zone, said congestion pricing "will put New York City at a disadvantage over competing cities and states, and businesses will flee".
Other big cities around the world, including London and Stockholm, have similar congestion pricing schemes, but this is the first in the US.
Proponents of the idea note the programs were largely unpopular when first implemented, gaining approval as the public felt benefits like faster bus speeds and less traffic.