Bowling all-rounder Harleen Deol, who plays for Himachal Pradesh in the domestic circuit, is set to replace Harmanpreet in the Mithali Raj-led one-day team.
Captain Harmanpreet Kaur, whose indifferent form has hurt the team, said she was disappointed at the result and the 0-3 series defeat.
New Zealand beat India by four wickets in the second T20I to take an unassailable 2-0 lead in the three-match series.
Chasing a modest target, New Zealand made heavy weather of the chase before scampering home off the last ball of the match losing six wickets.
Chasing 160, India were going strong at 102 for 1 but Smriti Mandhana and Jemimah Rodrigues' dismissal proved fatal for the visitors who collapsed to 136 all out.
The three-match series, which was part of the Women's ODI Championship, was won by India 2-1 but they suffered an eight-wicket loss at Hamilton on February 1.
The 33-year-old reached the milestone when she walked into the field for the ongoing third and final T20I against West Indies in Karachi.
In the second ODI against New Zealand, Mithali scored an unbeaten 63 off 111 balls as India chased down 162 in 35.2 overs.
The Indian women's team was at the centre of a huge controversy after its semi-final exit in the T20 World Cup owing to a bitter public spat between ODI captain Mithali and the then coach Powar.
The Indian women's team was at the centre of a huge controversy after its semi-final exit in the T20 World Cup in the West Indies.
The 29-year-old Harmanpreet said she was surprised to have been named the captain of the World T20 XI.
The selectors have reposed their faith on Mithali who retained her place in the T20 squad and captaincy for next month's tour to New Zealand.
The New Zealand tour will be the team's first assignment after its controversial exit from the World T20 last month when it lost to England in the semi-finals.
Mithali Raj and Romesh Powar were involved in a blame game after India crashed out of the Women's T20 World Cup in the semi-finals.
Harmanpreet and Smriti have already said that they want Powar to continue while Mithali is against his return.
In a letter written to Rai, COA member Edulji accused the chairman and BCCI CEO Rahul Johri of breaking rules while appointing Ravi Shastri as the men's team coach in July last year.
In her recent email skipper Harmanpreet backed former coach Ramesh Powar who has been targeted by Mithali over her exclusion from the squad.
On Monday, things became more dramatic with Harmanpreet throwing her weight behind the former spinner.
Harmanpreet and Smriti have made it clear that Powar alone wasn't behind Mithali's omission from the semifinal playing XI.
After Ramesh Powar's departure, it remains to be seen how T20 captain Harmanpreet Kaur and ODI captain Mithali Raj bury their differences.
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