The work by Richard Collins is believed to be the earliest known painting of the author and poet and captures him at the age of just four.
The portrait came to light at a recent valuation day held by the company in the Austrian capital Vienna.
It is now to go up for auction next month when it is expected to fetch between £3,000 and £5,000.
The portrait shows Scott as a child wearing a pale green coat, double-breasted white waistcoat over a frilled chemise and a black hat decorated with a ribbon bow.
Measuring less than two inches high, the painting is signed with the initials RC, dated 1775 and set in a rectangular leather travelling case in the form of a book.
'The portrait has emerged from the shadows of a private collection in Austria.' explained Bonhams' head of portrait miniatures, Camilla Seymour.
'It came to light on a recent valuation day in Vienna.'
The portrait's case carries a label attributing the work to Richard Cosway but it was in fact painted by his contemporary Richard Collins.
The miniature can be dated to 1775, when Scott visited Collins in London.
He was en route to the spa town of Bath in the hope of curing his lame right leg - the result of contracting polio, aged just two.
Scott was born in Edinburgh in 1771 but spent much of his life in the Scottish Borders where his historic home, Abbotsford House, is to be found.
He was the author of numerous famous works including Waverley, Rob Roy and Ivanhoe.
Text and image by BBC News, UK