Despite being contracted until the end of 2027, Gowans has paid the price for a second-straight season of finishing outside the top eight.
Starting the season 4-0, the Swans were one of the hottest teams largely on the back of Chloe Molloy's heroics.
But the superstar's season-ending back injury played a role in them losing six of their last eight games.
Molloy missed the shock defeat to Essendon in Coffs Harbour last Saturday that ensured they would miss finals.
Essendon had lost eight-straight matches before facing the Swans and were missing several key players.
Gowans, Sydney's inaugural AFLW coach, led the Swans to the semi-finals in just their second season.
He was given a contract extension in May 2024 following that breakout season.
Gowans can count himself unlucky for a second time given he was sacked by North Melbourne during the COVID-19 pandemic.
"Scott can be incredibly proud of his distinguished career as the senior coach of our AFLW team," Swans chief executive Matthew Pavlich said.
"Building a team from scratch is no small feat and we have seen that team grow and improve over the journey so far.
"Beyond his role as a coach, Scott has been a passionate advocate for women's sport.Â
"His tenure has been marked by vision, resilience and a commitment to empowering his players."
Gowans thanked Sydney for the opportunity of being a foundation coach.
"Building our list from scratch and guiding the team to where it is today is something I am incredibly proud of," he added.
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