Russian mission control confirmed the touchdown of NASA's Rubins, Roscosmos' Anatoly Ivanishin and Takuya Onishi of the Japan Aerospace Exploration Agency at 0358 GMT.
The trio landed southeast of the Kazakh steppe town of Zhezkazgan in frosty conditions after a flight from the orbital lab.
"Landing has taken place!" Russian mission control stated, with commentators on NASA TV noting that the Soyuz craft had landed in an upright position.
Molecular biologist Rubins and Onishi were both returning from their first missions in space, while flight commander Ivanishin also undertook a five-month mission at the ISS five years ago.
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The trio's arrival at the ISS was delayed by two weeks as Russian space officials carried out further software tests on the modified Soyuz MS-01 vehicle.
Rookie Rubins' participation in the mission generated particular excitement after NASA announced plans for the career scientist to sequence DNA aboard the ISS in a world first.
In August, Rubins successfully sequenced samples of mouse, virus and bacteria DNA using a device called MinION while Earth-based researchers simultaneously sequenced identical samples.
NASA said the biomolecule sequencer investigation could help identify potentially dangerous microbes aboard the ISS and diagnose illnesses in space.
The ISS space laboratory has been orbiting Earth at about 28,000 kilometres per hour since 1998.