Mr Bernstein, who is also chairman of the Football Association, said he had agreed to step down with immediate effect after 10 years in the role.
The decision comes after the Newcastle United owner's Sports Direct, which owns a 21% stake in Blacks, voted against his re-appointment at the the firm’s AGM last week. Its opposition comes after a 97% fall in the value of the company’s share since Sports Direct first invested in the chain in 2007.
At the weekend, a Sports Direct source was quoted as saying the company was "astonished" that Mr Bernstein was still in the job. The retailer - controlled by the Magpies owner - was reportedly considering a plan to call an extraordinary general meeting to oust Mr Bernstein.
Blacks said Mr Bernstein decided to step down because the company needed "a unified shareholder base" at a time of difficult trading.
It added: "During his time with the company, David has made a considerable contribution to the business and the board would like to take this opportunity to express their gratitude and to wish him well for the future."
Blacks recently negotiated a new £40m banking facility from Bank of Scotland, effectively giving it an extra £2m until December 15.
The move followed a "ignificant increase" in its debt after a worse than expected 9.7% drop in like-for-like sales in the 19 weeks to July 9.