Gregor Townsend’s side had been due to play the World Cup quarter-finalists last year but the game was called off due to Covid-related travelling restrictions.
The match with Japan will take place in Edinburgh on Saturday November 20 and completes a strong autumn line-up at Murrayfield.
They will likely be the first matches Scotland play in front of home fans in almost 20 months due to coronavirus.
Tickets are expected to go on sale in July, although three-match packages for the 2021 autumn internationals went on sale in December 2020 and have already sold out.
Japan will play at Murrayfield next month when they meet the British & Irish Lions on Saturday June 26 as part of the latter’s preparations for their upcoming tour of South Africa.
Scotland last played Japan at the 2019 World Cup in Yokohama when the tournament hosts won 28-21 to eliminate Townsend’s side at the group stage.
It was the Scots’ first defeat against the Brave Blossoms at Test level after seven previous victories, three of them coming in World Cup matches.
Kick-off times for the three autumn games have yet to be announced.
2021 Autumn Internationals at BT Murrayfield
Scotland v AUSTRALIA (Sunday 7 November)
Scotland v SOUTH AFRICA (Saturday 13 November)
Scotland v JAPAN (Saturday 20 November)