The United Nations estimates the crisis in the West African country affects around 5.2 million people, of which 1.6 million need urgent food assistance.
The cash will be targeted on the the Mopti region, where almost half of homes have insufficient food and humanitarian needs are said to have escalated most due to inter-community conflict.
Following a request by Scottish aid agencies working in Mopti, the funds are expected to go towards essential support such as food assistance, drinking water and hygiene campaigns.
Minister for International Development Ben Macpherson said: “The situation in Mali is very serious and this funding will provide aid to those most desperately in need.
“HEF member aid agencies on the ground, with extensive knowledge of the conflict, will work to ensure that this funding is targeted in order to maximise impact and alleviate suffering.
“Scotland is a compassionate, outward-looking nation and that is why, in demonstrating good global citizenship, the Scottish Government’s Humanitarian Emergency Fund provides essential aid to those in desperate need.”
He said he hoped the move will help galvanise others to assist those affected by the crisis.
The HEF panel comprises Tearfund, Oxfam, Save the Children, British Red Cross, SCIAF, Mercy Corps, Mission Aviation Fellowship, and Christian Aid.