He was accompanied by the Russian cosmonaut Yuri Malenchenko and American astronaut Peggy Whitson.
Ms Whitson - the space station's first female commander - and Mr Malenchenko are staying on the ISS for six months.
Mr Shukor spent nine days on the space station before returning to Earth with the outgoing crew.
The agreement for a Malaysian astronaut to fly to space was negotiated in 2003 as part of a commercial deal for Malaysia to buy 18 Russian fighter jets.
Mr Shukor's trip was paid for by the Malaysian government.
