As planned, the spacecraft's signal was lost for about 90 minutes as engineers turned it away from the sun and because the craft was moving too fast for its antennas to transmit.
The resumption of the craft's signal transmission was greeted with cheers from ESA engineers and technicians.
"We're extremely happy that it worked," mission manager Gerhard Schwehm said, sipping a glass of champagne after the announcement from the control room. "It's a big relief. People can relax a bit now and everything seems fine."
Schwehm said the agency would work to get images and other data collected by the probe processed as soon as possible. He said the first images should be released to the public Saturday.
"The operation went very well," Paolo Ferri, the head of the solar and planetary missions division and Rosetta flight operations director, said in a short speech after the announcement.
"The spacecraft is in exactly the condition we expected, which is good. All indications are that everything was super successful."
The timing of the flyby meant the asteroid was illuminated by the sun, making it likely the transmitted images will be clear and sharp for scientists working on the origins of the solar system.
"Dead rocks can say a lot," Schwehm said.
Astronomers have had to work with limited data from previous passes of asteroids, such as when ESA's Giotto probe swept by Halley's Comet in 1986, photographing long canyons, broad craters and 3,000-foot hills.
Steins was Rosetta's first scientific target as flies in the asteroid belt between the orbits of Mars and Jupiter en route to its main destination, the comet 67/P Churyumov-Gerasimenko, which is scheduled for 2014. The probe was launched in March 2004.
The European Space Agency is supported by 17 countries, including Germany, France, Ireland and the Netherlands. It cooperates with NASA, the European Union, European national space agencies and international partners.