After landing, Shkaplerov ate from a bowl of grapes and said he was feeling well and happy to be back on Earth.
Earlier footage from the ISS showed Shkaplerov and a fellow cosmonaut practising with the ball.
They are set to land in Kazakhstan around 1240 GMT after having spent 168 days in space.
In the opening match of the world championship on football of 2018 which will be held on June 14 in Moscow, the teams will play the ball had been in space, RIA Novosti reported.
During his stay at the ISS, he conducted various scientific experiments as the 12th Japanese astronaut to travel into space and the seventh to stay at the ISS for a period of months.
Kanai of the Japan Aerospace Exploration Agency made life on the space station more accessible to Japanese-speakers by tweeting in the language most days.
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Scott Tingle, who was on his first flight, experienced a spacewalk with the mission to replace the hand of one of the station's robotic arms.
NASA astronaut Serena Aunon-Chancellor, Roscosmos cosmonaut Sergey Prokopyev and German astronaut Alexander Gerst are preparing to go to the ISS this week.
The three had been on the orbital laboratory since mid-December, with Shkaplerov, 46, serving as mission commander from February until he turned over command to American Drew Feustel on Saturday.
Around 9:40 p.m. on June 3 Japan time, Kanai, 41, landed safely in a steppe near Jezkazgan in central Kazakhstan aboard the Russian space capsule Soyuz, along with two other astronauts from Russia and the United States.
The ISS passes into the dark side of the earth for roughly half of each of its 90-minute orbits.
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