Jeju United defender Baek Dong-Gyu, an unused substitute, sprinted from the bench to throw an elbow at Urawa Reds captain Yuki Abe as tempers flared at the end of the last week's game in Saitama.
Trailing 2-0 after the first leg in Jeju, the Japanese won 3-0 at home to advance to the quarter-finals but the tie ended in bitter acrimony as players squared up to each other after the final whistle.
"Baek wanted to meet Abe in person to apologise," a Jeju official told South Korea's Yonhap news agency.
"He is set to visit Japan in the near future," the official added.
"Baek apparently thought his team-mates were hit by Urawa players, so he threw an elbow. Baek was in agony after he realised that the family of the player he struck was at the stadium."
The 26-year-old Baek is not the first player to court controversy in matches involving South Korea's fierce rivalry with Japan.
Park Jong-Woo caused a blazing diplomatic row after waving a political sign following South Korea's 2-0 victory over Japan in the bronze medal game at the 2012 London Olympics.
A year later at the East Asian Cup, South Korea fans unfurled a banner declaring "A nation that forgets its history has no future" -- a reference to what many Koreans see as Japan's refusal to acknowledge its wartime aggression.
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