With this latest mission Russian space veteran Malenchenko has spent a total of 827 days in orbit, according Russian space agency Roscosmos.
Malenchenko ranks second for the record number of days spent in space, trailing behind his compatriot Gennady Padalka who has spent 878 days in orbit, Roscosmos said.
Peake, Malenchenko and Kopra had blasted off into space from the Baikonur Cosmodrome in Kazakhstan in December.
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At around 0215 GMT, they bid farewell to NASA astronaut Jeff Williams and Russian cosmonauts Oleg Skripochka and Alexey Ovchinin, who remain aboard the ISS.
Their Soyuz TMA-19M spacecraft then undocked from the ISS, Roscosmos said.
Peake's mission has generated great excitement in Britain, where the government unveiled an ambitious new space policy on the eve of his departure for the International Space Station.
Peake's time in space was marked by a number of milestones. In January, he became the first Briton to walk in space, undertaking a mission to replace an electrical unit.
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In April he ran a marathon in space in record time, strapped into a treadmill while thousands ran the London Marathon.
Peake managed to achieve the fastest ever marathon in space by marking a time of three hours, 35 minutes and 21 seconds, setting a Guinness World Record.
The next launch of astronauts from the Baikonur cosmodrome is scheduled to take place on July 7.
It will take Anatoly Ivanishin of Russia, Kate Rubins of the United States and Takuya Onishi of Japan to the ISS.