The organisation said it would accept Mr Haskell's immediate resignation. Its chairperson, Lynn Weidner and two other executives are also leaving.
The emails reportedly include vulgar references to past winners and comments about their sex lives.
Former contestants criticised the "appalling" revelations.
The organisation's president and chief operating officer, Josh Randle, has also resigned "in light of recent and new developments", a spokesperson confirmed to the BBC.
Announcing the resignation of Mr Haskell in a statement posted on its Twitter account, the Miss America Organisation (MAO) said Ms Weidner would help install a new leadership before leaving.
Board member Tammy Haddad resigned on Friday.
The announcement of Mr Haskell's resignation came only hours after the MAO put out a statement saying he had been suspended.
The Huffington Post published the alleged contents of three years of emailsbetween Mr Haskell and other pageant officials.
The internal emails include name-calling, slut-shaming and fat-shaming of some of the contestants who had taken part in the pageant.
The revelations caused Dick Clark Productions, MAO's television sponsor, to cut ties with the long-standing pageant.
Dick Clark Productions said in a statement on Friday they had been made aware of the emails "several months ago" and were "appalled by their unacceptable content".
Pressure for the resignation of Mr Haskell also came from 49 former Miss Americas in an open letter.