Pfau, 87, died on August 10 after spending 57 years to working to eradicate leprosy, tuberculosis and other diseases in Pakistan.
Pfau, born in Leipzig, in 1929, arrived in Karachi in 1960 en route to India and volunteered at a local leprosy colony.
While in Karachi, she became depressed at the state of the care given to patients whose hands and feet she said had become "nutritional supplement for the rats," according to the Marie Adelaide Leprosy Centre's (MALC) website.
Prime Minister Shahid Khaqan Abbasi had earlier announced a state funeral for Dr Pfau, saying: "The entire nation is indebted to Ruth Pfau for her selflessness and unmatched services for eradication of leprosy."
Pakistani military personnel carried the casket containing Dr Pfau's body into St Patrick's Cathedral in Karachi's Saddar area.
Her casket, draped in the national flag of Pakistan, was given a 19-gun salute, with contingents of all three armed forces present on the occasion.