The money will be provided to charities working in the African nation, which is at risk of famine due to the combined effects of conflict, climate change and Covid-19.
The Scottish Catholic International Aid Fund (SCIAF) and Christian Aid will deliver emergency food, seed kits, field crops and agricultural training to people with disabilities.
Money from the government’s Humanitarian Emergency Fund will also be used to spread coronavirus awareness and prevention.
Earlier this year, the UN warned that South Sudan is facing its highest levels of food insecurity and malnutrition since its independence a decade ago.
International Development Minister Jenny Gilruth said: “The situation in South Sudan is a desperate one, and we stand ready to act when confronted with such a pressing emergency.
“We know that more than 7 million people, more than half the population, face hunger – and this is where the Humanitarian Emergency Fund can play a part.
“The Scottish Government is committed to fulfilling its role as a responsible and compassionate global citizen and this aid will provide essential help to those in desperate need.”
SCIAF chief executive Alistair Dutton said: “We are proud to be a part of the Scottish Government’s Humanitarian Emergency Fund.
“With this funding, we will help people with disabilities in South Sudan receive the emergency food they desperately need.
“We are working with our local partners to provide vital seed kits and field crops, alongside agricultural training, to help families survive this crisis and build a better future.”