Captain Alfred George Freeman, who went on to captain other Ellerman Lines ships including the SS City of Singapore and a newer SS City of Pretoria from 29 November 1950 to 26 November 1960, was her Chief Officer from 6 August 1939 to 16 August 1939.

The U-boat torpedoed the City of Pretoria, causing her to explode and sink northwest of the Azores.

All aboard her, including her master, 108 crew, 24 DEMS gunners, five apprentices and seven passengers were lost with her.

The passengers were "Distressed British Seamen" (DBS) being repatriated to the UK because their former ships had been sunk.

One of the passengers was James Allistair Whyte, previously third officer of City of Cairo, who had survived 51 days in a lifeboat after she had been torpedoed and sunk by U-68 on 6 November 1942.