The last-placed Saints will conduct a review into their AFLW program, led by former Carlton football boss Brad Lloyd, in the wake of Dal Santo's departure.
Dal Santo, a St Kilda great as a player, was in his sixth season at the Saints and will coach his final game against Collingwood on Saturday, before departing
"I've been giving a lot of thought to my future and whether continuing in this role was the right decision, both for myself and the program," Dal Santo said in a statement.
"Where we've been able to take this program is something I'll always be incredibly proud of.
"It's been a privilege to coach this group and help shape its formative years in the competition.
"I have a strong love for this club, I wanted to contribute to women's football, and with a daughter of my own, it's great to see a pathway for young females with football ambitions.
"I'm looking forward to finishing my time as coach alongside the group this weekend and wish them every success for what comes next."
The Saints will have three games left in the season after Saturday, when they will attempt to amend their unwanted record of being the only winless team in the competition.
"Nick has made a significant contribution to our AFLW program across six seasons and will always be an important part of our football club," St Kilda chief executive Carl Dilena said in a statement
"His care, commitment and leadership have been unwavering, and we thank him for everything he has given to the program, including leading the team to its maiden final's appearance last season.
"We look forward to recognising Nick's contribution this weekend as he leads the team one final time in front of our members and supporters at RSEA Park."
Lloyd will lead the review, via Apogee Sports, during the remainder of the season, while the Saints start their hunt for their next coach.
"Our ambition is to be a consistently competitive and respected club that can contend with the best in the competition," Dilena said.
"We want to give our AFLW program every chance to achieve this and that means identifying where we need to improve, investing in the right areas and acting with urgency."
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