The Glasgow musician picked up the Â£20,000 prize for his album Thirteen Lost & Found during an award ceremony at the city's Barrowland Ballroom.
Hubbert, known as Hubby, whose album includes collaboration with other artists, said: "I am shocked and delighted at winning."
Nine other artists were shortlisted for the award.
The contenders included Django Django, Karine Polwart, Admiral Fallow, The Twilight Sad, Lau and Stanley Odd.
The original longlist of 20 albums had included Emeli Sande's Our Version of Events and 18 Months by Calvin Harris, two of the best-selling albums in the world last year.
The award, developed by the Scottish Music Industry Association, was judged by a panel which included Glasgow University music expert John Williamson, broadcaster Douglas Anderson, author Christopher Brookmyre, artist Douglas Gordon and music critic Sue Wilson.
Mr Williamson, chairman of the judging panel, said: "All of the albums had supporters among the judges and the final decision was extremely close.
"Among the things that impressed across the range of albums were the range of emotions and quality of songwriting. All of these are records made in a modern way without big budgets or big productions and all involved degrees of collaboration and community with other musicians from Scotland and beyond.
"In the view of the judges, RM Hubbert's album was the one that encapsulated and engaged the most."
Guitarist RM Hubbert has won this year's Scottish Album of the Year award.