People entering the country from the two Baltic states must self-isolate for 14 days upon arrival as of 4am on Saturday.
The Scottish Government said it comes after a “significant increase in cases” of coronavirus and a rise in the numbers testing positive.
Justice Secretary Humza Yousaf said: “We continue to closely monitor the status of the pandemic in countries across the world, given circumstances can change so rapidly and that all of us must take great care to avoid contributing to the spread of the virus.
“Our message remains clear that people should think very hard before committing to non-essential foreign travel as the public health situation, and therefore our response to it, can change rapidly.
“It is imperative that we disrupt the spread of this virus, which remains a significant challenge in Scotland and across the world.”
Air bridges have also been opened in a several areas after health officials deemed Covid-19 cases are at a safe level.
These include Aruba, Bhutan, Israel, Jerusalem, Kiribati, Micronesia, Mongolia, Namibia, Northern Mariana Islands, Rwanda, Samoa, Solomon Islands, Sri Lanka, Timor-Leste,
Tonga, Uruguay, Vanuatu and the Caribbean islands of the US Virgin Islands, Bonaire, Sint Eustatius and Saba.
The enhanced travel controls that prevented visitors arriving into the UK from Denmark will also be removed this Saturday but people will still be required to isolate for 14 days.
Mr Yousaf commented that the removal of Denmark and addition of a number of destinations should not be taken as ‘green light’ for overseas travel.