An initial 72 applicants made written applications which were shortlisted to the top 20, who then pitched to a panel of judges, and were narrowed down to seven finalists.
Since early May they have s been preparing to pitch for their spot in the top three, having been involved in a series of workshops.
Startup Dunedin chairwoman Sarah Ramsay said the high quality of applicants exceeded expectations.
"It's fantastic to see startups from a variety of backgrounds, innovating in a variety of fields," she said.
The three Challenger finalists, announced on Thursday night, are Next Farm, a Dunedin-based agritech startup creating autonomous irrigation to enhance water management practices, maximising farm yields while minimising inputs.
The company Winely delivers winemakers timely data by automating the collection and analysis of data during winemaking, while Kaffelogic has developed a home coffee bean roaster, using sophisticated software alongside elegant design, to make 100g-batch coffee roasts.
"Given Dunedin's rich history of manufacturing, it's also heartening to note this year all the winners are physical products," Mrs Ramsay said.
The final phase of the Challenger Series begins on June 24 and will include five months of mentoring and support from some of Dunedin's top business leaders as the businesses ramp up.
She said the Challenger Series services startups already had some traction and were looking to scale up and grow.
All finalists will receive $15,000 worth of support, including $5000 credits from both Deloitte and Gallaway Cook Allan, plus $5000 cash support from Startup Dunedin.
Startup head starter Donna Hall said some of the unsuccessful applicants were completing the nine-week Co.Starters programme and she hoped they would apply for the 2020 Challenger Series.
Deloitte partner Kyle Cameron said it was great to see a group of talented people, driven to succeed in business.
"All of the short-listed entrants had clearly articulated a market need for their offering, and to me that was a clear indicator of the maturity of this group of entrants," he said.
The Challenger Series was a collaboration including the Dunedin City Council's Enterprise Dunedin, Grow Dunedin Partners, Startup Dunedin, Creative HQ, Callaghan Innovation, Deloitte and Gallaway Cook Allan.
- The judging panel was Pete Hodgson, chairman of Callaghan Innovation, New Zealand Trade & Enterprise investment manager Tamsin Bateman, Deloitte partner Kyle Cameron and Forsyth Barr senior investment adviser John Gallaher.