Mott takes over after James Hopes quit last month to join Brisbane Heat, 53 days after being appointed successor to Greg Shipperd.
The perennial contenders were disappointed by the false start, but have secured a top-tier replacement in 52-year-old Mott.
He spent seven years as head coach of the Australian national women's team, winning four Ashes series, two Twenty20 World Cup titles and a 50-over World Cup.
On his watch, Australia set a new world record for the longest winning streak in one day internationals for either a men's or women's team, claiming 26 straight victories between 2018 and 2021.
His tenure came at a crucial time for the women's game, which was navigating the transition to the professional era.
Mott has since served as head coach of England's men's white-ball sides between 2022 and 2024, winning the T20 World Cup during his first year in charge.
At BBL level, Mott has served as an assistant coach at the Sixers for the past two summers and also coached their WBBL team last season.
The Sixers are expected to announce their new WBBL head coach later this week.
Mott has signed a two-year deal with the Sixers, who made last year's grand final but lost to the Perth Scorchers.
"I've been part of the Sixers family for a long time, so to have the opportunity to step into the BBL head coach role is something I'm incredibly excited about," Mott said.
"This is a club with a proud history and a winning culture and I'm looking forward to building on the foundations that have been established over many seasons."
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