After blown away for a mere 76, Anil Kumble's team saw the Proteas amassing 494 for seven before unseasonal rain brought the second day's play to a premature close.
A B de Villiers with an unbeaten 217 and Jacques Kallis with 132 were the tormentors-in-chief. Already behind by 418, the weather seems to be the only ray of hope for the hosts.
"A western distubance over Rajasthan and Gujarat has caused induced circulation, bringing rains to the northern and central parts of Gujarat," Kamajit Ray, Director of the Indian Meteorological Department said.
Rain and thunderstorms can be expected in the northern and central regions of the state for the next 24 hours, Ray added.
The Sardar Patel Stadium in Motera, the venue for the Test, falls in the Central Gujarat region.