More than half (52%) of people put the tree in first place in the three-month consultation run by Forestry Commission Scotland.
The rowan came second with 15% of votes, while the holly was third with 7%.
Forestry Commission Scotland is now developing a funding package and a range of activities to help raise the profile of the Scots pine, such as projects with schools, conferences and seminars. More than 4500 people responded to the consultation.
Environment and Climate Change Minister Paul Wheelhouse said: "Scotland's trees, forests and woodlands are some of our greatest and most treasured natural assets. We are rightly proud of them because they help shape our landscape.
"The Scots pine was an obvious choice and certainly the people's choice. Its designation of being the national tree of Scotland will help create an iconic symbol to highlight the significant contribution trees make to our country."
The idea of a national tree came from Alex Hamilton, a member of the public who brought his campaign to the Scottish Parliament through a petition.
He said: "I look forward to this symbol of our beautiful and life-giving woodlands being embraced by all."