The SRU announced today that Johnson would continue in his current role for the summer tournament with Italy, Samoa and South Africa, but would then be replaced.
SRU chief executive Mark Dodson said: "It's imperative that we get the right candidate as head coach of the national team to take us to the 2015 Rugby World Cup and Scott and I are working together on this and have thought long and hard about the best solution and people for Scottish Rugby to continue to head in the right direction.
"Johnno has been a popular coach with the players, as underlined by our third place finish in the most recent RBS 6 Nations Championship."
The 50-year-old joined the Scotland coaching team last year following the end of a three-year spell with Ospreys as director of coaching. He took over as head coach on an interim basis after Andy Robinson's resignation last November.
Johnson said in the SRU statement: "The director of rugby job excites me. It's about making a really positive contribution that will stand Scottish Rugby in good stead for years to come and I am looking forward to the challenge of the new role as well as continuing with the Scotland team."
He has also coached Wales and USA.