The unusual hijacking took place at a traffic light in the city of Mthatha in Eastern Cape province on Tuesday night, police spokesman Mzukisi Fatyela told SAPA news agency.
A pair of armed men hijacked the first hearse and drove off in it, only to become stuck in mud in a nearby village.
They then abandoned the vehicle and headed directly for the funeral parlour.
There they overpowered a guard and made off with another hearse, loaded with specialist equipment including casket-lowering devices.
Fatyela said the hijackers must have known what they were looking for:
"We strongly believe that someone operating a funeral parlour is behind this hijacking, it is unusual to hijack a hearse."
The investigation continues.