The move comes following a successful reintroduction trial from 2009 to 2014.
From today it is an offence to kill or harm beavers and destroy their dams and lodges, except under special licence.
There are about 450 wild beavers living in two separate populations in Scotland – in Argyll, where the trial was carried out, and in Tayside, where a large colony has sprung up from escaped or illegally released animals.
Conservationists say the legal protection is an important step that will enable the species to spread naturally across the country.
Beavers create new wetlands, which support otters, water voles and dragonflies, and help to regulate flooding and reinvigorate woodland, according to the Scottish Wildlife Trust.
Chief executive Jo Pike said: “Beavers are unrivalled as ecosystem engineers. They have the potential to greatly increase the health and resilience of our natural environment by creating new habitats.
“Granting beavers protected status is an important milestone for the return of the species to Scotland’s lochs and rivers. It follows decades of work by countless organisations and individuals to demonstrate the positive impacts that beavers can have.”
Barbara Smith, chief executive of the Royal Zoological Society of Scotland, hailed it as a “historic day for Scotland”.
Beavers offer widespread ecological and social benefits, including increasing biodiversity, reducing flood risk and creating new opportunities for wildlife tourism.
However, their reappearance has sparked conflict due to their impact on agricultural land and damage to valuable trees. Dozens – including pregnant and nursing females – have been shot as a result.
NFU Scotland stressed that management and licensing schemes for the species must be “workable” and let land workers deal with problems.
Member Angus MacFadyen, who farms in Argyll, said: “Beavers can have negative impacts, especially when they occur in highly productive agricultural areas. As such, the beaver population is already causing many farmers great concern because of the way that beavers can undermine river banks and flood banks and potentially impede farmland drainage.”