Coach Gary Stead will also sit out the January tour, with his assistant Luke Ronchi to take charge of a squad to contest three ODIs followed by three T20Is.
Southee will lead the team on their forthcoming tour of Pakistan with Tests in Karachi, starting on December 26, then in Multan beginning on January 3.
Team India will be up against the Kiwis in the third and final game of the three-match ODI series, on Wednesday, November 30, from 7:00 AM onwards at Hagley Oval, Christchurch.
Dhawan-led team India will be up against the Kiwis in a three-match ODI series, with the first ODI on Friday, November 25, from 7:00 AM onwards at Eden Park, Auckland.
The Kiwis will be up against the Men in Blue in the third and final T20I of the three-match T20I series on Tuesday, November 22, from 12 PM IST onwards at Napier.
The Kiwis will be up against the Men in Blue in the 2nd T20I of the three-match T20I series on Sunday, November 20, from 12 PM IST onwards at Mount Maunganui.
The Kiwis will be up against the Men in Blue in the 1st T20I of the three-match T20I series on Friday, November 18, from 12 PM IST onwards at Wellington.