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The Kelvin and Aimee Tyler-trained 5yr-old flashed home along the outside running rail to nail the favourite, Orepuki Lad, on the line to take out the 2147m feature at $42 odds.
The victory provided rider Tanya Jonker with two milestones to celebrate.
The South African-born apprentice scored her first group or listed race win and brought up her 50th riding victory in New Zealand.
Jonker was not about to celebrate either of those achievements until the judge, Brendon Burke, announced Lil Miss Swiss as the winner.
"I didn't think I had got it," the jockey said.
"I was just really happy with her [Lil Miss Swiss'] performance and the way she pushed herself at the end.
"She's got a big heart and it paid off."
Lil Miss Swiss looked in big trouble when four lengths off the back of the field before the home turn.
Jonker asked the mare to make up that ground from the 500m and she angled Lil Miss Swiss to the extreme outside of the track.
Once she balanced in the straight, Lil Miss Swiss produced a scintillating late finish to deny Orepuki Lad.
"It's kind of her style and works for her when she gets a clear run," Jonker said.
"I just didn't know if she had the wheels to beat some of the really good horses in the race today."
Orepuki Lad had a break of about 15 lengths on Lil Miss Swiss at the 500m.
The Graham and Michael Eade-trained stayer cruised to the front on the home turn and looked to have the race won, but was denied his third southern cup win by just a nose.
The Tyler-trained Kilowatt rallied well to take third place.
Lil Miss Swiss provided Aimee Tyler with her first group or listed race win on a big day for her stable.
The Tyler stable produced He's Got Power to win Saturday's 2yr-old event, race 1, and Valetina Vittoria to win in rating 65 company in race 9.
The Riverton trainers are well represented on the second day of their home track's Easter meeting today.
Lil Miss Swiss, Timy Tyler and Tilly Dunnage represent the stable in middle-distance feature the Riverton Highway Stakes over 2147m.
Class prevailed in Saturday's fillies and mares feature, the Francolin Stakes.
Multiple feature race-winner Kiwi Ida again proved she was lethal over her pet distance of 1400m when scoring for trainers John and Karen Parsons and rider Tina Comignaghi.