The funding will provide 760,000 people in urgent need with food vouchers, as the east African nation suffers it's worst food crisis in a decade.
James Wharton also praised the response of organisations such as the Scottish Catholic International Aid Fund (Sciaf) and Mary Meals to the situation, which has been triggered by drought.
The minister said: "Scottish NGO's such as Sciaf and Mary's Meals are playing a vital role in the UK Government's work to prevent and prepare for the impact of El Nino by providing lifesaving food, water and shelter to people in urgent need."
Relations between Scotland and Malawi span 158 years and several Scottish charities focus their efforts in the country.
Westminster and Hollyrood have already pledged millions of pounds to support humanitarian work in Malawi, with the UK government recently awarding more than £6.7 million to Mary's Meals and Sciaf to support women farmers and help feed children.
David Hope-Jones, principal officer of the Scotland Malawi Partnership, said: "We welcome this strong continued commitment from DFID [the Department for International Development] to support some of the poorest and most vulnerable communities in Malawi at this critical time of food shortage."