During the Stormers' Investec Super Rugby loss to the Blues earlier in March, flanker du Toit suffered a haematoma that developed into an acute compartment syndrome.
It is a rare condition in which only 43 cases have been listed in medical literature around the world.
Stormers' team doctor Jason Suter told South African media, "It's a medical emergency because if you don't pick it up early they lose blood supply to the leg and they lose the leg.
"Within 15 minutes of him coming off the field and assessing him, we realised that he was at risk of this particular rare condition.
"He was taken straight to Vincent Pallotti [Hospital] where he had a vascular surgeon waiting and he was operated on that night.
"It's very unusual, very rare, but they had to cut through the muscle to release the pressure and they were only able to close that leg 10 days after his initial injury," he said.
Du Toit has been released from the hospital and was recuperating at home. Had rugby still been being played he would have been out for three months.
Stormers coach John Dobson said Suter deserved enormous credit.
"Had a rugby player lost his leg it would have been devastating for the game. And if it wasn't for the timely intervention then I think [he could have lost his leg]…almost half of the 43 reported cases had resulted in that," he said.
The cessation of Super Rugby had come at the right time for the Stormers who reported other serious injuries.
World Cup-winning prop Steven Kitshoff is out of action for four months after tearing his pectoral muscle which requires surgery.
Halfback Herschel Jantjies, another member of the World Cup squad, broke his arm and is likely to be out of action for three months. Springbok captain and flanker Siya Kolisi was still a month away from starting his return-to-play protocols after a medial ligament tear while hooker Bongi Mbonambi, who tore off his hamstring is expected to be out for another four or five months.