As expected, Johnson has linked up with new Wallabies boss John Connolly, signing a three-year deal as attack coach which will see him return Down Under next month.
He has been acting head coach for Wales since the shock departure of Mike Ruddock in February and cut a very popular figure with players, who hoped he would take up the position on a permanent basis.
"I have loved every single moment of my time here in Wales - it is one of the greatest rugby communities and countries in the world. It has become my home and I will be sorry to leave," said Johnson.
"It is not been an easy decision for me to reach but, for once, I have had to put my family first. I've always been open and honest with the WRU, the Welsh players and the Welsh public on this issue and I would have loved to have stayed had it been possible.
"The way in which the Welsh players have responded to the work I've done with them has been fantastic. They are a very special group and Wales hasn't seen the best of them yet.
"When Graham Henry first invited me to come to Wales to join his coaching team I didn't really know what I was letting myself in for.
"Since then, and having worked so closely with Steve Hansen, Alan Phillips, Mike Ruddock, Andrew Hore, Clive Griffiths and the rest of the Wales management team, I have enjoyed a life changing experience which I wouldn't change for anything.
"I left my family on the other side of the world to work in Welsh rugby and, as I said after the game against France, I have no regrets.
"I wish the new head coach all the luck in the world and the management team continued success. As for the Welsh players I've worked with, they know how I feel about them.
"The Welsh fans were always superb towards me and I will never forget the special bond they struck with their team. There is a lesson in that for every sporting nation.
"I will miss Wales, the Millennium Stadium and all my friends here. But the time has come to move on and, just as Welsh rugby is currently doing, I will now focus firmly on my future.
"I would love the opportunity to come back to Welsh rugby in some capacity in the near future as I could think of no better place to settle."
WRU chief executive Steve Lewis added: "Scott never made any secret of the issues that would ultimately determine whether or not he would seek to stay in Wales at the end of his current two-year contract.
"The personal issues he has to resolve have mitigated against him seeking to extend his stay in Wales. On behalf of the WRU, I would like to thank him for the important role he played both as a skills coach under Steve Hansen and Mike Ruddock and as the interim Head Coach in recent months.
"Scott made it clear to us he would not be applying for the Head Coach role and, as a result, any extension of his position within the Welsh coaching team would have been in the hands of whoever is appointed by the WRU.
"However, it is plain for all to see that the impact he has had on the international players he has worked with since coming to Wales in 2003 has had a hugely beneficial effect on them."