The emergency occurred as the first and second stages of a booster rocket separated shortly after launch from Kazakhstan's Soviet-era cosmodrome of Baikonur.
The Soyuz MS-10 rocket had four first-stage boosters strapped to its central core, which housed the second stage booster. They were met by rescue teams in remote Kazakhstan more than 200 miles from their launchpad at the Baikonur Cosmodrome.
"The breakup of the Soyuz", Kommersant broadsheet said in a frontpage headline, while Nezavisimaya Gazeta daily wrote: "The space industry crashed in a couple of minutes".
There was no immediate word on whether Mr Gertz and the current space station crew might need to extend their own six-month missions.
Images show the Soyuz-FG rocket booster lifting the Soyuz MS-10 spacecraft high into the sky before Thursday's mission was abandoned.
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The Russian Soyuz spacecraft is now the only vehicle for ferrying crews to the International Space Station following the retirement of the USA space shuttle fleet.
The two-man US-Russian crew of a Soyuz spacecraft taking them to the orbiting International Space Station had to make a dramatic emergency landing in Kazakhstan yesterday when a rocket failed in mid-air. Russia's Investigative Committee said it had opened a criminal investigation into the matter.
Relations between Moscow and Washington have sunk to post-Cold War lows over the crisis in Ukraine, the war in Syria and allegations of Russian meddling in the 2016 USA presidential vote, but they have maintained co-operation in space research.
In a letter to the Russian space agency released Thursday, ESA director general Johann-Dietrich Worner praised the "extreme reliability" of the Soyuz and its importance for all countries with space programmes.
Rogozin has complained of problems with NASA and has suggested that a hole on the ISS could be the result of sabotage.
Until the investigations are completed, there will be no official information about what caused the rocket's failure to carry the crew to orbit.
"As we wait for the conclusions of a Russian probe, the Soyuz will perhaps be grounded for some time", he told AFP.