One scientist confirmed the good news: "We have a healthy spacecraft".
A series of anxiously awaited "phone home" signals arrived after 10:30 am (1530 GMT), indicating that the spacecraft had made it, intact, through the risky, high-speed encounter.
Lead scientist Alan Stern of Southwest Research Institute in Boulder, Colorado, expects the New Year's encounter to be riskier and more hard than the rendezvous with Pluto: The spacecraft is older, the target is smaller, the flyby is closer and the distance from us is greater.
At 12:33 a.m. EST on January 1, 2019, more than four billion miles from Earth, a NASA spacecraft launched in January 2006 will fly within 2,200 miles of an ancient planetary body, orbiting more than 40 times the distance from the Earth to the sun and undisturbed for perhaps billions of years.
"This is a night none of us are going to forget", said Queen guitarist Brian May - who also holds an advanced degree in astrophysics - and who recorded a solo track to honor the spacecraft and its spirit of exploration.
New Horizons, which is the size of a baby grand piano and part of an $800 million mission, was expected to hurtle to within 2,200 miles (3,500 kilometers) of Ultima Thule, considerably closer than the Pluto encounter of 2015.
Stern said that Ultima Thule was unique because it was a relic from the early days of the solar system and could provide answers about the origins of other planets.
These bodies are time capsules, preserved in a deep freeze for the past 4.6 billion years.
The object is so old and pristine that it's essentially like going back in time to the beginning of our solar system.
What does it look like?. More news: Montrezl Harrell after win over Lakers: 'There's two teams in LA'
More news: Fox News commentator and writer dies suddenly, aged 26
More news: Lampert's hedge fund says bid submitted to save Sears
Scientists are not sure what Ultima Thule (pronounced TOO-lee) looks like - whether it is cratered or smooth, or even if it is a single object or a cluster.
It was discovered in 2014 with the help of the Hubble Space Telescope, and is believed to be 19-32km in size. New Horizons had to perform a 140 seconds flyby at a distance of 75 by 200 miles (120 by 320 kilometer) around the object.
Hal Weaver, a research professor at Johns Hopkins University in Maryland and a project scientist on the New Horizons mission, said: "It's a once-in-a-lifetime opportunity".
Scientists at NASA are celebrating after receiving messages from its New Horizons probe, 6.5 billion km away.
In classic and medieval literature, Thule was the most distant, northernmost place beyond the known world.
Icy wilderness: The object lies in the Kuiper Belt, a huge area of mysterious chunks of ice and small planet-like objects that lies way beyond Neptune, and a billion miles further on than Pluto.
"There's a lot of chatter in the science team room", Spencer said.
"This is another great step in the exploration of our solar system". "We'll find out Tuesday".
The confirmation isn't just a relief for the New Horizons team.
In fact, retrieving information from New Horizons is so delayed that even NASA doesn't know with certainty that the spacecraft pulled off its mission without a hitch.