The Pope sent a telegram of condolence to Cardinal Kim's successor, Cardinal Nicholas Cheong Jinsuk.
One of the nation's most revered religious leaders, Cardinal Kim was a champion of human rights and a promoter of democracy in the face of strong military dictatorships.
An official of the Seoul Diocese reported the cardinal had been hospitalized since last year, and that he died of frail health. The diocese reported that the cardinal's last words were "thank you."
Benedict XVI wrote in his message that he was "deeply saddened to learn of the death of Cardinal Stephen Kim Sou-Hwan, I offer heartfelt condolences to you and to all the people of Korea."
The Pontiff continued: "Recalling with gratitude Cardinal Kim's long years of devoted service to the Catholic community in Seoul and his many years of faithful assistance to the Holy Father as a member of the College of Cardinals, I join you in praying that God our merciful Father will grant him the reward of his labors and welcome his noble soul into the joy and peace of the heavenly Kingdom.
"To Cardinal Kim's relatives and all assembled for the solemn mass of Christian burial, I cordially impart my apostolic blessing as a pledge of consolation and strength in the Lord."
Stephen Kim Sou-hwan was born to a Catholic family in Daegu, Korea. He was the youngest of seven siblings.
Kim was ordained a priest in 1951 and was named bishop of Masan in 1966. In 1968 he was appointed archbishop of Seoul, and one year later elevated to cardinal. At 47, he was the youngest member of the College of Cardinals at that time.
Cardinal Kim retired in 1998.
Archdiocese of Seoul will hold the cardinal's funeral service Feb. 20, after five days of memorial Masses.
With his death, the College of Cardinals now has 188 members, including 115 electors and 73 non-electors.