Simona Frapporti (Bepink) stunned the big names, winning the final criterium from a break that unusually stayed away after escaping mid way through the race. The Italian beat Lauren Stephens (Tibco) and Rushlee Buchanan (New Zealand) to the punch.
But Winder and her Trek-Segafredo team mates did enough to defend her lead despite contesting and losing the first intermediate sprint to closest GC rival Liane Lipper (Sunweb) which saw her slim lead reduce to just five seconds.
Lippert didn't have enough in the tank at the next contest especially when Trek-Segafredo sent their sprint star Lotta Henttala to claim the maximum seconds.
"That (stage) was pretty crazy. I used to do a lot of crit racing when I was young in the US, but it's been a bit of a while since I've done a really hard one like that," Winder said.
"Sunweb and Mitchelton are really strong teams, but we were able to pull it off and I'm really excited.
"(On Saturday) after winning the stage it was such a great feeling and I'm really excited to celebrate with my team."
It is the first time in five editions iterations of Mitchelton-Scott has not won the Women's Tour Down Under, katrin Garfoot winning in 2016 and Spratt claiming the other three.
Despite her reign coming to an end, the newly crowned Australian road champion managed third overall at just six seconds behind Winder.
“Of course I came here to win but I’m really proud of the third place. My reign at the Tour Down Under had to end at some point.
"I can’t fault the team this week, they all rode really well. There wasn’t much more that we could have changed, we were just beaten by a stronger rider, especially on yesterday’s stage.
“It was a different Tour this year, it all came down to bonus seconds. That made it quite exciting and it put me out of my comfort zone today too.”