Ferguson will leave Old Trafford after 26 years in charge, and Bernstein believes that the 71-year-old has had a career that should be celebrated.
The 69-year-old told the Football Association's official website: "Sir Alex Ferguson's achievements are truly remarkable – he is genuinely one of the greatest managers of all time and certainly of the modern era.
"His contribution to English football has been outstanding in every regard and, in the FA's 150th year, it is something that should be celebrated. On behalf of the FA I'd like to wish him a happy and healthy retirement."
The Scot will leave Old Trafford after leading the club to their 13th Premier League title.