Crowds gathered at John Hopkins Applied Physics Laboratory to listen for the 'phone home' signal which was sent from the probe 5 billion kilometers away from Earth.
The mission team confirmed the successful flyby of Pluto on Twitter.
New Horizons Mission Operations Manager Alice Bowman says the probe has collected data using its recorder.
"It was very happy to go on and collect more science and the main computer system has the data recorder and our CNDH engineer had reported the expected number of segments on that recorder had been used and so that tells us that data has been collected on the space craft."
NASA's New Horizons craft performed the flyby of Pluto at nearly 12,500 kilometers above the planet's surface making it the closest approach to the dwarf planet ever.
The unmanned probe launched 9 years ago has travelled 5 billion kilometers of space to reach Pluto and all of the images and measurements taken will be transmitted back in 16 months' time.
NASA Administrator Charles Bolden explains the significance of the Pluto Flyby.
"NASA as an agency is on a journey to Mars with other agencies around the world. And every mission in science and exploration is expanding our knowledge of our solar system and our universe and helping pave the way for the next space craft in human missions to the farthest destinations. Today's mission was just one more step on the journey of getting humans to Mars because it gives us one more piece of the puzzle about our solar system."
For his part, NASA Associate Administrator John Grunsfeld, says there's still a long way to go.
"If you think it was big today, wait until tomorrow and the next day. We haven't seen anything yet. This is really just the beginning. This is the equivalent of the Curiosity Rover landing. It's the beginning of the mission even after almost a decade in transit and many more years of attempts to get a Pluto mission and then once Pluto New Horizons was selected and was being built, who could have imagined that we'd all be here with a successful encounter of Pluto."
The probe will not orbit or land on Pluto but head deeper into the Kuiper Belt, a region scientists believe to be filled with hundreds of small, icy objects.
Kuiber Belt objects are believed to prove the early formation of the solar system.
For CRI, I'm Xie Cheng.
