Nitschke will take charge for the T20I tri-series in Ireland in June which also features Pakistan then the Commonwealth Games in Birmingham. It buys CA time to appoint a new full-time coach ahead of the home season although Nitschke will be well placed to take the job.
She was appointed assistant coach of the Australian women's team in 2018, having previously spent time with South Australia and Adelaide Strikers. In 2019, she took charge of Perth Scorchers in the WBBL, leading the team to its maiden WBBL title last summer.
On leaving his position, Mott said he felt "honoured" to have been in the Australia role for a seven-year period which in recent years has brought unprecedented success with back-to-back T20 World Cup titles and the ODI World Cup last month in New Zealand.
"I leave with a heavy heart but with so many wonderful memories," he said. "The on-field success is well documented but it's the lifelong friendships that I've formed that resonate most with me. I am very proud to have been part of a sport that has been able to endure the last couple of years and come through it with an even brighter future.
"There is never a perfect time to leave such a wonderful environment, but this opportunity is one that excites me very much.
"To all the support staff, players, and administrators both past and present, thank you for all your support and guidance during my time with the team. Not all coaches get to leave on a high and I have nothing but gratitude and admiration for everyone who has helped me in this amazing experience over my tenure with this great team.
"This playing group is led magnificently by a number of players, including Meg [Lanning] and Rach [Haynes], who have together helped forge a culture which will thrive for many years to come. I wish the team all the best and look forward to seeing them grow what's become an incredible legacy."
Cricket Australia chief executive Nick Hockley paid tribute to the success Mott has helped forge on the field and also the impact in growing the game at lower levels.
"Under Matthew's leadership, the team has claimed every major trophy on offer and importantly, has inspired kids across the country to pick up a bat and ball," he said. "He should be proud of the legacy he's helped create with our women's team.
Ben Oliver, general manager of national teams, added: "Matthew's appointment is richly deserved and reflects the global standing and dominance of the Australian women's team which he has guided over the past seven years."