Police were accompanying the coyote, which was walking in the bike path along Hudson River Park.
They followed the coyote into an outdoor parking lot, near Watts Street.
Members of the NYPD's elite Emergency Services Unit tranquilized the coyote and pulled it out from under a red car in the parking garage
It was placed into an animal carrier, and taken to the ESU vehicle.
The sighting was not far from where the coyote was seen and lost by police yesterday afternoon.
This was the fourth coyote sighting in New York City over the last few weeks.
This one was first spotted coming out of the Holland Tunnel on Wednesday afternoon, according to people using Twitter who witnessed police chasing the coyote.
The Port Authority could not confirm if the coyote was actually in the tunnel.
The coyote was seen again later at Warren and Greenwich Streets, heading south on Varick Street and on Thomas Street.
That's where Eyewitness News spotted police surrounding the coyote in TriBeCa, but the animal ran off yet again.
Earlier this month, a coyote was spotted in Chelsea around West 24th Street and 12th Avenue.
Just last month, students and residents reported sighting of three coyotes on Columbia University's campus.