Jaco Rossouw, 34, is in a critical condition after sustaining 95% burn wounds in the incident, which took place at about 09:00 on Sunday morning.
The petrol attendant sustained burns to his own arms in the process. He is being treated in hospital under police guard.
Shocked motorists at the garage put out the flames on Rossouw's body with a fire extinguisher. He was treated by paramedics and rushed to Warmbaths provincial hospital in Bela-Bela before being transported by helicopter to Muelmed Hospital in Pretoria on Sunday afternoon.
A friend, Mark Harper, said late on Sunday night that "he is not doing well at all. The doctors only bring bad news but we hope and trust that God will perform a miracle".
The petrol attendant and Rossouw had apparently had a row. It is not clear what it was about, but some of the other petrol attendants said Rossouw had fired him.
Police spokesperson Lieutenant Colonel Malesela Ledwaba said after the row, the petrol attendant threw petrol into a bottle, set it alight and threw it through the window of the office building.
Natasja Kotze was heading back to Meyerton from Polokwane on Sunday morning when she stopped at the fuel station. "You never think you will experience something like that. It was awful to see."
Kotze said they saw how the badly burnt Rossouw was treated by emergency rescue workers outside the office section of the fuel station. They also saw the petrol attendant in a police van.
Kotze said some of the petrol attendants told them their colleague had threatened to throw petrol through Rossouw's office window earlier on Sunday morning. "They then stopped him and said they didn't see him pouring petrol in the bottle later."
Trompie Jonker of the private Tromar ambulance service said the fire extinguisher that bystanders used to put out the flames on Rossouw's body, caused him to inhale some of the substance sprayed by the extinguisher. It also badly damaged his lungs.
Rossouw stopped breathing while emergency workers from Tromar as well as the provincial ambulance workers treated him. "His hair, eyelashes and almost all his skin was burnt off. His lungs and windpipe were also damaged by the smoke he inhaled," said Jonker.
Ledwaba said the attendant would appear in court this week on charges of attempted murder, arson and theft of petrol.
Rossouw and his wife, Edna, live in Bela-Bela. They have two young children, Ruben, 4, and Emma, 2. His wife was with him in hospital on Sunday evening.
She wrote on her Facebook page on February 7: "Seven wonderful years together, my husband! You are a gift from God to me and the children! Couldn't have asked for a better man!! Love you lots."