A total of £5 million will be invested in Interface, which connects firms with colleges, universities and research organisations.
The programme, which was established in 2005, will receive the investment from the Scottish Funding Council, Scottish Enterprise and Highlands and Islands Enterprise.
Companies supported by Interface contribute an estimated £64.2 million (gross value added) to the economy each year.
The programme has introduced almost 3,000 businesses to academic partners.
First Minister Nicola Sturgeon announced the funding at the official opening of the Roslin Innovation Centre, where she also met businesses that had benefited from the Interface service.
She said: “Scotland is home to some of the most highly-rated research institutions in the world and we continue to invest to ensure this leads to practical industry innovation.
“This further investment from the Scottish Funding Council and the enterprise agencies in Interface will help to amplify our talent and expertise by connecting national and international industry with all of Scotland’s universities, research institutes and colleges.
“This boosts productivity, profits and exports - and creates jobs - and many companies that have benefited from Interface funding say their project would not have happened without its support.
“This additional £5 million will help nurture links between world-leading research and innovation, which provide a competitive edge for industry and supports valuable inward investment and exports.”
Dr Siobhan Jordan, director of Interface, said: “There is huge potential in partnering businesses with our world-leading academic institutes to develop creative solutions for commercial problems.
“Businesses don’t always know how to tap into academic expertise - this funding will ensure that Interface can continue to make valuable connections leading to transformational collaborative research and development.
“By fostering new connections between industry and academia we can tackle economic and societal challenges in innovative ways.”