The 69-year-old was appointed Football Association chairman in January 2011 but will not be able to serve a full three-year term according to the governing body's rules
The FA Board convened on Wednesday in order to vote on whether Bernstein would be allowed to continue but decided that the rules regarding the maximum age of those in senior positions could not be amended on an individual basis.
The St Helens-born business executive was appointed to the role in January 2011 but will now have to step down in May 2013, the month of his 70th birthday.
Bernstein told the FA's official website: “I respect the decision and I remain committed to fulfilling my responsibilities and to building on what we have achieved over the past two years.
"Next year is a significant one in The FA's history and I look forward to leading the organisation in the months ahead.”
Bernstein, who replaced Lord Triesman in the role, led recent efforts to boycott Sepp Blatter's re-election as Fifa chairman following the suspension of Mohammed Bin Hammam.
He also previously held the position of chairman at Manchester City between 1998 and 2003.