More than 400,000 people have lost their homes and at least an estimated 480 lives have been lost as a result of Cyclone Idai.
An appeal launched by the Disasters Emergency Committee (DEC) on Thursday to help those affected raised £8 million within its first 24 hours.
International Development Minister Ben Macpherson announced that the Scottish Government would provide £150,000 to the appeal.
Around £100,000 of funding is to come from the international development budget, with £50,000 allocated from the Climate Justice Fund to support emergency flood relief in Malawi in securing water supplies and treating contamination.
Earlier this month, the Scottish Government pledged a total of £175,000 towards supporting relief efforts.
“Our thoughts are with all of those affected by the terrible consequences of Cyclone Idai,” said Mr Macpherson.
“As an outward-looking, compassionate country it is right that we do what we can to support the international response to this humanitarian emergency.
“This funding will help aid agencies in Malawi, Mozambique and Zimbabwe to deliver life-saving support to local families and communities in desperate need, as will all public donations to the DEC Scotland appeal.”
Sally Foster Fulton, of Christian Aid and DEC Scotland, said: “The DEC in Scotland is delighted that the Scottish Government has made available this extra funding.
“The Scottish public are already responding generously, as always, and we’re sure this extra boost will inspire others to dig deep in the coming days.
“The response from our members and partners on the ground over the weekend will be vital in saving and protecting lives, so please donate now.”