Widely known as Pakistan's Mother Teresa, Pfau died last week in the southern city of Karachi at age 87. She is to be buried in her adopted homeland.
Mourners paid their last respects as Pfau's coffin was carried to the Marie Adelaide Leprosy Centre that she founded before being taken on to St. Patrick's Cathedral for the official service.
Pfau had been living in Pakistan since 1960, and her leprosy centre in Karachi was Pakistan's first hospital dedicated to treating the disease. She later opened treatment centres across the country.
"It is a big loss to this hospital and to humanity. It is very hard to find a person like her in today's era," said Yasmeen Morris, a staff member at the centre.
"She led a very simple life and she loved humanity."
In 1996, the World Health Organisation declared that leprosy had been controlled in Pakistan, which led Pfau to the more challenging task of eliminating the disease.
Last year, the number of patients under treatment for leprosy fell to 531 from over 19,000 in the 1980s.
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