The crew had to abort.
American Nick Hague and Russian Alexey Ovchinin landed safely after an "anomaly with the booster" prompted the ascent to be aborted, NASA head Jim Bridenstine said in a statement.
Hague and Ovchinin were to join the current three-person crew on the International Space Station to perform research experiments. "Today showed again what an awesome vehicle the Soyuz is, to be able to save the crew from such a failure".
Russian Federation was forming a state commission to investigate the Soyuz launch incident, Nasa said.
Vladimir Titov and Gennady Strekalov survived a fire during launch in Kazakhstan in 1983.
The politician has clashed with the U.S., suggesting American astronauts should use trampolines instead of Russian rockets to reach the ISS after Washington imposed sanctions over Moscow's 2014 annexation of Crimea.
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They were set to join the crew of Alexander Gerst, the station's first-ever German commander, as well as USA astronaut Serena Aunon-Chancellor and Russian cosmonaut Sergei Prokopyev. The missions both hope to launch in 2019, though they have each experienced delays thus far.
Manned space launches have been suspended pending an investigation.
Speaking with reporters in Moscow before Thursday's launch, Bridenstine said that Russian-American cooperation in space remained strong, amid an investigation into the cause of the leak.
Had the launch gone smoothly, Ovchinin and Hague would have reached the space station later today.
A transport plane dropped a team of paratroopers to the site to make first contact with the crew, while helicopters were dispatched to pick up the astronauts. This is especially tricky, as the new batteries arrived later than expected after a series of launch delays from the Japanese cargo vehicle they were on.
Those precious few minutes of elation in Peabody quickly turned into an agonizing wait, as NASA confirmed there had been a booster problem with the rocket and the crew had to make an emergency exit.
Gerst took the opportunity to point out that the Soyuz spacecraft is "an wonderful vehicle", as it was able to save the crew after its booster failure. But exactly when the astronauts will be sent home is still unclear.
Today's failed Soyuz launch thankfully resulted in no casualties, but the fate of the International Space Station (ISS) is now in question.