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Production will end this summer, said the Swiss group.
The Willy Wonka line was relaunched late last summer accompanied by a £3.6 million marketing campaign.
At the time of the launch, Nestle said it was looking to build a sustainable brand of chocolate bars.
The Wonka product is available in 100g sizes and comes in three flavours.
Although retail sales exceeded £16 million to May 24, according to IRI figures, sales began to fall off from an initial £3 million per month to around £1 million per month.
Consumers love novelty and innovation in confectionery and this sits perfectly with a brand such as Wonka, said Nestle this month.
The chocolate brand will still be available in UK and Irish food stores for much of this year.