WARSAW — Cardinal Franciszek Macharski, a popular Polish prelate who served for many years as archbishop of Krakow, inheriting the position opened by the election of Pope John Paul II, died on Tuesday. He was 89.

Cardinal Macharski held one of the top positions in Poland’s Catholic Church in an era when the church played a leading role in opposing the communist system — action that helped to undermine the regime’s authority in the eyes of many Poles.

The death of Cardinal Macharski, who had been close to John Paul and was deeply respected, comes five days after Pope Francis stopped by his hospital in Krakow to pray for him during a visit last week to Poland. Cardinal Macharski was hospitalized in June and was unconscious at the time of Francis’ visit.

From the Vatican, Francis wrote that he received the news of Cardinal Macharski’s death ‘‘with pain.’’ In a letter to the current Krakow archbishop, Cardinal Stanislaw Dziwisz, Francis said that Cardinal Macharski ‘‘guided the church in Krakow in the not easy period of political and social changes with wisdom.’’

In Krakow, the Royal Sigismund Bell at the Wawel Cathedral tolled for several minutes. The bell is a national symbol that only tolls on certain feast days and national holidays and is otherwise reserved for special occasions.

Cardinal Macharski was appointed Krakow archbishop in 1978 by John Paul, who had held the position himself until he was elected pope earlier that year. Cardinal Macharski served as archbishop until 2005, retiring two months after John Paul died.