Dziwisz was appointed titular bishop of San Leone and joint head of the Prefecture of the Papal Household on February 7, 1998. He was ordained a bishop on March 19 of that year, the principal consecrator being Pope John Paul II, and the co-consecrators Angelo Sodano, Secretary of State and Franciszek Macharski, the then Archbishop of Kraków. John Paul II elevated Dziwisz to the rank of archbishop on September 29, 2003, still having the titular see of San Leone.
Dziwisz has written a book, scheduled for release on March 4, 2008, entitled A Life with Karol: My Forty-Year Friendship with the Man Who Became Pope.
As John Paul's private secretary, Dziwisz issued many statements from the Vatican, occasionally clarifying situations, as in the case of The Passion of the Christ. When John Paul was quoted as saying "It is as it was", possibly suggesting that he supported the controversial Mel Gibson movie, Dziwisz told the press that, "The Holy Father has told no one of his opinion of this film."
Many people said that John Paul and Dziwisz had a father-son like relationship. He slept in a bedroom next to that of John Paul's, was always near him during Mass, and was with him almost every waking moment. During John Paul's papacy, he became one of the most influential voices in the Vatican.
As the health of John Paul declined, some speculated that in light of being one of John Paul's most trusted aides Dziwisz may have been preparing the faithful for the worst. The Roman newspaper Il Messaggero reported that Archbishop Dziwisz mentioned his concern to another Polish priest. According to Vatican sources Dziwisz told the priest, "Pray for the pope, because he's getting worse."
On March 31, 2005 John Paul's condition became serious enough that Archbishop Dziwisz administered the Anointing of the Sick to the Pope. Before the death of John Paul, Dziwisz was reported to have helped him write a message to his staff not to grieve, that he (John Paul) was happy and that they should be too.
When John Paul died on April 2, 2005, Archbishop Dziwisz was at his bedside. According to rules created by John Paul, Dziwisz packed his belongings and was forced to vacate the papal apartments before they were sealed by the camerlengo. It was believed that John Paul had hoped to appoint Archbishop Dziwisz as Archbishop of Krakow and elevate him to become a Cardinal Priest, a post and title the pope had held. A vacancy did not however occur before John Paul's death. It was Pope Benedict XVI who named Dziwisz to the post of Archbishop of Krakow, and later elevated him to cardinal.
During the Mass of Requiem on April 8 for John Paul, Archbishop Dziwisz had the honor of placing a white silk veil over the face of the Pope before the body was lowered into three separate caskets. It was the symbolic last act of service of Archbishop Dziwisz as papal secretary for John Paul.
On June 3, 2005, Benedict XVI appointed Dziwisz as successor to the retiring Macharski as Archbishop of Krakow. It had been suggested that John Paul II has been grooming Dziwisz for the position and was merely waiting for Macharski to retire before making such an appointment. Benedict XVI is believed to have made the appointment as one of the last wishes of John Paul II. At the consistory of March 24, 2006, Archbishop Dziwisz was raised to the cardinalate, becoming the Cardinal Priest of the Titulus S. Mariae de Populo. It is customary to name the bishops of certain important episcopal sees, such as Kraków, to the College of Cardinals. Dziwisz had also been mentioned as the possible secret cardinal in pectore appointed by John Paul II in 2003, but the pope took this secret to the grave. Dziwisz's elevation to the cardinalate will allow him to participate in any upcoming papal conclaves until his 80th birthday in 2019.