"The Catholic church has lost its father," said Father Achilles Kasozi, during a solemn mass at the Sacred Heart church late Monday to pay tribute to the pontiff, who died Saturday.
A picture of John Paul, adorned with 10 candles, rested against the altar in front of the faithful, some of them shedding tears.
Kasozi urged worshippers to "pray that we may serve the Church as John Paul II did" and to continue praying at home "that his soul may rest in eternal peace."
More than 800 members of the Sudanese community, many of them refugees, attended the mass, including James Gore.
"He was a man of peace and he always remembered Sudan in his prayers," said Gore of the late pope, a man many Sudanese Christians cherish for his stance against injustice and oppression around the world.
"The pope saw the suffering of our people first hand."
John Paul II visited Khartoum in 1993 at the height of the civil war between the mainly Arab and Muslim north and the animist and Christian south, denouncing the use of violence in the name of religion.
"The only struggle which religious motives can justify, the only struggle worthy of man, is the moral struggle against man's own disordered passions," the pope had said.
"When people are weak and poor and defenseless, I must raise my voice on their behalf," he said.
"When they are homeless and suffering the consequences of drought, famine, disease and the devastations of war, I must be close to them and appeal on their behalf to those who can offer help," he added.
His visit emboldened the country's Christians, as they resisted the jihad, or holy war, declared against them by Sudan's ruling Islamic fundamentalists.
It motivated many, including Willma John, to serve in the church.
Many also converted to Catholicism at a time when the church was losing its members to Islam and to evangelical Protestant churches.
"It really strengthened the Catholic Church in Sudan," John said after the service, adding that she had hoped Sudanese Christians would do more to honor John Paul II for the many blessings he bestowed on them.
The pope also gave Sudan its first saint in October 2000 -- Josephine Bakhita.
Bakhita was born into a wealthy family in the western Darfur region in 1868 and kidnapped by slave traders when she was nine. She was eventually bought by the Italian consul, who took her back to Italy, where he freed her and she worked as a nanny for his family.
She eventually converted and joined the Institute of the Canossian Daughters of Charity order, which she served for 50 years. She was known for her gentle presence and willingness to help with any menial task and for her comfort to the poor and suffering.
In another first for Sudan, the pope made Khartoum Archbishop Gabriel Zubeir Wako a cardinal in 2003.