The £3.8m fund will help cover costs incurred from weather which devastated the area in December 2015 to January 2016.
The money comes on top of a previous £2.39m allocated to the council last year, which saw over 200 households and businesses received £1,500 grant payments, and 38 businesses received grants of £3,000.
The funding will also be used to progress work on a flood protection scheme in Hawick.
Announcing the money during a visit last week, Energy Minister Paul Wheelhouse said: "There's no doubt that the Scottish Borders was among the areas hit the hardest by last year's flooding which is why this £3.8 million of funding will be welcome news to the council and communities affected by the storms. I witnessed the effect of the flooding in Hawick during Storm ‘Desmond' and I know how traumatic it was for many here and in communities elsewhere in the Borders affected by the floods.
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"This support through the Bellwin scheme will help Scottish Borders Council meet the majority of the immediate and unforeseen costs of the flood damage and supplements help to 200 households and many local businesses.
"The Scottish Government is committed to working to reduce flood risk across Scotland and has committed £420 million over the next 10 years to protect homes in many of our most flood-prone areas including the future Hawick Flood Protection Scheme."
Cllr Gordon Edgar added: "I am delighted that the Scottish Government has supported this Council by releasing the full funding we applied for through the Bellwin scheme for the eligible costs we incurred during and following last winter's storms.
"The scale of the damage to the region's roads, buildings, parks, open spaces, footpaths and bridges was quite simply the biggest challenge we have ever had to date.
"Many of the repair works were challenging and time consuming and I would like to thank our staff for their efforts, and the public for their patience and understanding during what was an extremely difficult and challenging time for the Borders and the Council.
"In the 12 months since Storm Desmond, two flood schemes have been completed in the Scottish Borders and the Hawick scheme is getting closer to entering its next phase before construction. We welcome the continued support from the Scottish Government on these projects too."
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