Earlier Friday, Yuzuru Hanyu withdrew from the event after injuring his ankle in practice, a setback that could have a serious impact on his preparations for an Olympic title defense.
Italy's Carolina Kostner, the victor of the 2007 and 2010 competitions, was runner-up with 212.24, followed by Russian Polina Tsurskaya (210.19) in the 12-woman field at Osaka Municipal Central Gymnasium.
"In my country, a veteran is a respected person, a veteran of the war for example", he said.
"The most important thing is that you love what you are doing".
Sixth after Friday's short program, Japan's Satoko Miyahara (191.80) had two under-rotated jumps but pulled off a solid performance to claim 126.75 for her routine to finish fifth.
Israel's Alexei Bychenko sits in second place with 85.52 points and United States' Jason Brown third with 85.36.
The home favourite sustained an injury to his right foot when he fell in practice yesterday afternoon.
Morocco book World Cup place for first time in two decades
Congo beat Guinea 3-1 in a whirlwind finish, when Congo scored twice in injury time, but that still wasn't enough. While Tunisia held on to a 0-0 draw against Libya to make their first World Cup appearance since 2006.
"Whenever I skate in Japan, I can bet on being cheered by a warm audience, and this time I was able to skate in good condition", Medvedeva said. "Unfortunately the doctors have made their final decision that I should not take part". "I will now go through treatment as I prepare for the Japanese nationals".
Medvedeva gave a dramatic performance to the music of "Anna Karenina" and scored 144.40 points in free skating despite falling on her opening triple flip. Japan's Kazuki Tomono (231.93) was sixth, while compatriot Hiroaki Sato was 11th with 199.20.
China's reigning world champions Sui Wenjing/Han Cong claimed the NHK Trophy pairs title after breaking a record of free skating score on Saturday.
The Japanese Nationals take place December 20-24 and the Japan Olympic team will be announced afterward.
Five-time European champion Carolina Kostner of Italy ranked third in free skating with 137.67 points, but held on to overall second place on 212.24 points.
Russia's Olympic silver medallists Ksenia Stolbova/Fedor Klimov came second while their teammates Kristina Astakhova/Alexei Rogonov placed the third.