Holley, who has been with the Ospreys since their inception in 2003, will leave the organisation with immediate effect following discussions with the board over the future direction of the region which has led to a top-to-toe review of the coaching set-up.
Speaking about his decision to step down now, rather than at the end of the season as previously announced, Johnson commented: "After talking through the issues facing the business with the Board, we've come to a decision that is for the good of the organisation as a whole, which means that I'll be giving up my post with immediate effect.
"I was brought in to a job for the Ospreys, with a particular a remit to help set-up systems that would enable us to bring through home grown talent, coaches and players, and we agree that I'm leaving an organisation that is now better equipped to deal with the challenging times that lie ahead for all the Welsh regions.
"When I informed the Board in December that I wouldn't be renewing my contract, I made the offer to stand down at that time but they felt that it would be better for the organisation if I remained in office to help provide some stability during what was inevitably going to something of a transitional period.
"Since then we've been in constant dialogue and six weeks down the line, we've agreed that the time is right for me to move on so we've shaken hands and I'm walking away early from the remainder of my contract.
"I'll leave with only happy memories from my time with the Ospreys and I've made some great mates for life among the business. For me personally, the next few months will allow me to head back to Australia to catch up with my family and to get over the illness that I've suffered with over the last two years, before taking up the post with Scotland at the end of the season."
Andrew Hore, Chief Operations Officer at the Ospreys, added: "After extensive discussions, Scott has offered to step down from his post now rather than at the end of the season, and we have agreed to release him from the remaining terms of his contract. It was a gesture that he has made for the good of the Ospreys business and is typical of the way he has continuously put the region first during his three years as Director of Coaching.
"He will be greatly missed by everybody at the Ospreys, but the time is right for a fresh start, and by agreeing to move on now, it means that both the business and Scott can start to look forward to the future.
"Scott leaves a positive legacy behind, having been influential in putting in place new player and coach development structures while also having to deal with reducing the wage bill for the long-term good of the business, which will help ensure the long term sustainability of Ospreys Rugby."
Holley commented: "The Ospreys will always be my home region. It's been a rollercoaster of a ride but I can honestly say I have thrived on it, put my heart and soul into it and tried to embrace it. I could not have survived the constant expectation and pressure that comes with the job without the support of my family and friends, many of our true supporters, and in particular the team management and the players."