MSP's have voted in favour of the Land and Buildings Transaction Tax (LBTT) (Amendment) (Scotland) Bill.
The new ruling means a supplement will be implemented on buying additional homes such as second homes or buy-to-let properties.
Deputy First Minister John Swinney proposed the amendment in a bid to protect first time buyers in Scotland.
In addition, Chancellor George Osbourne revealed a similar charge would be introduced by the UK Government from 01 April 2016.
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The supplement is 3% of the total price of the property for all purchases above £40,000 and is payable in addition to the current LBTT rates.
Mr Swinney said the Scottish Government's priority is to give first time buyers the "greatest possible chance" to get on the property ladder.
"That is why I decided to act to avoid any potential distortions that could arise in Scotland from the new higher rates of stamp duty land tax payable on the purchase of additional residential properties, announced by the Chancellor of the Exchequer in his Autumn Statement on 25 November 2015," he said.
"This is particularly relevant to the purchase of additional residential properties, at the lower end of the market, which could make it more attractive to invest in such properties in Scotland compared to other parts of the UK.
"Our LBTT additional homes supplement will ensure that opportunities for first time buyers to enter the housing market in Scotland remain as strong as they possibly can."
The amendment will take effect from 01 April.
(LM/CD)
