The funding comes one year after the University of London said it was to close.
The base is now expected to re-open in February with the new money.
North Ayrshire Council has been awarded a total of £500,000 from the Regeneration Capital Grant Fund, which is run jointly and funded by the Government and COSLA, with an additional £500,000 being allocated by the Scottish Funding Council to Glasgow University for their role in delivering services.
Cabinet Secretary for Education and Lifelong Learning Michael Russell explained: "Over the last few months we have worked very hard with partners including North Ayrshire Council, COSLA, the University of Glasgow and the Field Studies Council to find a sustainable way to rescue the Millport marine base and safeguard its contribution to the local economy.
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"Those efforts are paying off and I am delighted that the Scottish Government has been able to provide a total of £1 million to help secure the future of the base. The station is expected to re-open, under new owners, in February and this is a significant success for all those who have played a role in developing plans."
Councillor David O'Neill, President of COSLA added: "The Millport marine base is one of the projects funded from the first year of operation of the joint COSLA and Scottish Government Regeneration Capital Grant Fund. This fund helps improve physical, economic and social outcomes for communities, resulting in long term strategic and transformational change.
"I am pleased to see this funding contributing to the future of the Millport marine base. The involvement of the community in partnering North Ayrshire in seeking to prevent further local loss of key employment on the island and the delivery of positive regeneration outcomes was a key aspect of the project being successful in securing funding, and of which they should be rightly proud."
(JP)
