Colin de Grandhomme (105) and Tom Blundell (107) helped themselves to centuries as the Black Caps posted 520-9 declared in response to the tourists' 134 before skittling the Windies for 319 from 231-2.
An ICC statement confirmed: "The Windies were ruled to be three overs short of their target after time allowances were taken into consideration."
It is Holder's second offence in a 12-month window, prompting his ban.
As well as missing the second Test, which begins in Hamilton on Saturday, Holder has been fined 60 per cent of his match fee. The rest of the Windies players have been docked 30 per cent.
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