Tributes have been paid to the toddler after the tragedy, which occurred on the 70-time capped legend’s 39th birthday.
Du Plessis has two older daughters with wife Ronel – Rosalie and Hele. Lions chief Rudolf Straeuli confirmed the news and appealed for the family’s privacy.
South Africa are preparing to face England on Saturday and Springboks’ number eight revealed the news had been received at the international camp.
"We haven't discussed it as a squad, yet, but I woke up to a message from my missus about what had happened back home," he said.
"They are in our thoughts and on our minds, and we send our condolences to Jannie and family.
"It's obviously a very difficult time and we will stand behind and support them in whatever way we can."