The 50-year-old takes over Andy Robinson whose three-year tenure ended last month following a poor run of results.
Johnson, a former Australian Under-21 international, joined Scotland this year as an assistant coach following a stint at Welsh club Ospreys.
"Scott has a wealth of experience of international rugby, which was instrumental in his appointment earlier this year as our senior assistant coach," Scottish Rugby CEO Mark Dodson said in a statement on the union's website (www.scottishrugby.org) on Thursday.
"He has coached with Australia, Wales and the USA and knows what it is to prepare teams to win on the international battleground."
The Scotland role will be Johnson's second as an interim head coach. He led Wales in three tests in 2006.
"It's an honour to take charge of the national team for our imminent campaign," Johnson said.
"I will be doing everything I can to bring the best out of our players as we all seek to achieve winning performances."
Johnson's first match in charge with be Scotland's Six Nations opener against England at Twickenham on Feb. 2. (Writing by Tom Bartlett, editing by Ed Osmond)