A spokesperson confirmed the move, saying it was in line with its retail network strategy.
Rumours were rife mid last year that the store would be closing down, but in May David Jones insisted it had no plans to change its store operations in New Zealand.
The Australian retail giant first expanded into New Zealand in July 2016 with the opening of its Wellington store in an iconic Lambton Quay building that once housed the Kirkcaldie & Stains department store.
Its Auckland store was more than three years in the making after David Jones had originally planned to enter the market in the City of Sails but due to real estate availability, launched in the capital.
The Newmarket store will remain open.
A David Jones spokesperson said the retailer remained committed to serving customers in New Zealand and, along with its Auckland store, looked forward to introducing online offerings in the second half of 2022.
"As the retail sector continues to transform, including the accelerated shift to online, the optimisation of our retail network – through investment in our digital and physical channels, a focus on right-sizing and where necessary, consolidation of our physical footprint – is critical to meeting the changing needs of our customers."
The spokesperson said the decision to close the Wellington store was not made lightly.
"We sincerely thank our customers and our team for their support and commitment."