The 24-year-old Cell C Sharks prop replaces the unfortunate Trevor Nyakane who tore his right calf in the 23-13 defeat by New Zealand in Yokohama on Saturday night.
Du Toit, who was on a short-term loan to Toulouse, was on standby and had been involved in preparations right up until the team’s departure for Japan.
He is expected to join the squad in Nagoya on Tuesday afternoon.
“It’s very tough on Trevor,” said Rassie Erasmus, director of rugby. “He has had a great season and added value whenever he took the field. It’s a blow to him and the team, but it’s also an opportunity for Thomas and for Vincent [Koch] who now have the chance to step up.”
The Springboks continue their Rugby World Cup campaign against neighbours Namibia in Nagoya on Saturday (kick off 11h45 SA time).