Apologising to his fans for "making them worry," Olympic champion Hanyu reluctantly dropped out of the NHK Trophy after falling and injuring his right leg in practice on Thursday, scuppering his chances of appearing in the grand prix final in Japan next month.
Chan had earlier withdrawn to devote himself to practice after a disappointing finish in Skate Canada, the second of six grand prix events.
Japan's grand prix is the fourth of the six qualifying events for the International Skating Union's Grand Prix Final in Japan in December, two months before the start of the Winter Olympics in Pyeongchang, South Korea.
Skating to the tango-influenced beat of "Adios Nonino" by Astor Piazzolla, the 30-year-old Voronov wowed the crowd in the western city of Osaka with the height of his jumps, which included a clean quad toeloop and triple toeloop combination as well as a triple axel.
A two-time Russian national champion and the bronze medallist in the 2014-2015 grand prix final, Voronov's score of 90.06 narrowly missed his personal best of 90.33 and put him nearly five points ahead of second-place Alexei Bychenko of Israel. Jason Brown of the United States finished third.
Hanyu said in a statement that he would focus on healing and preparing for the Japanese nationals in late December, but the injury could eat into practice time for Pyeongchang, where he hopes to be the first man in 66 years to win back-to-back golds.
World champion Medvedeva performed a flawless routine to Frederic Chopin's "Nocturne", landing a clean series of triple jumps in an elegant, flowing performance to take the lead with 79.99, just under her season's best.
"It was an okay performance, I could have done some things better, such as the double axel," Medvedeva said. "I want to do a perfect routine tomorrow and bring joy to the fans."
Medvedeva was followed by Italy's Carolina Kostner and compatriot Polina Tsurskaya in third.
World pairs champions Wenjing Sui and Cong Han of China skated to the lead with 79.43 points, followed by Ksenia Stolbova and Fedor Klimov of Russia.
(Reporting by Elaine Lies; Editing by Toby Davis)
