The shoes, which launched as a limited-edition "retro" range two years ago, are based on a design from 1988 and carry the logo "Runnin' 'n' Gunnin".
The sportswear giant is to take the £90 shoe, which has been a big seller, out of distribution. It is no longer available to buy on Nike's official website, although other retailers are still selling it.
A spokesman for Nike said the name was not a reference to knives but had become an "unfortunate coincidence" given the surge in knife-related crimes.
He explained the shoe was first launched in 1988 as a stability running shoe, which is where the word "stab" was derived from in the product's name.
He said: "We completely reject the idea that we are in any way condoning or encouraging the issue of knife usage.
"At any given time, Nike has thousands of shoes in the market, each with an individual name - it would be impossible to name them all based on future assumptions about news stories. Given the current climate, however, we have withdrawn the shoe from our Nike Town store."
However, the company continues to sell a range called Pocketknife online, as part of its all-weather ACG range.
Hannah Daws, a spokeswoman for the crime-fighting charity Crimestoppers, told Brand Republic: "The charity Crimestoppers is astonished that a major retailer such as Nike could be this naive and act so irresponsibly with its marketing by naming its products 'Air Stab' and 'Pocketknife'.
"With the current gun and knife epidemic that is sweeping our country we would expect retailers to be taking a more sensitive approach to promoting its products to a young and impressionable market."
The move by Nike comes 11 days after staff at the company's flagship store in London's West End were themselves the victims of knife crime.
Two security guards were attacked at Nike Town with knives as they tried to apprehend a gang of teenage shoplifters, suffering stab wounds to their legs and backs.
Nike's decision to withdraw the Air Stab shoe follows widespread concern about a knife crime epidemic. So far this year, 53 people have been stabbed to death in London alone.
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