The 61-year-old admitted a Football Association charge in relation to betting offences on Tuesday.
Moore was suspended by Tranmere back in February as the FA began its investigation into whether he had breached betting rules.
"Tranmere Rovers will not tolerate any action that damages the integrity of this football club," Tranmere operations director and club secretary Mick Horton told the club's official website. "Any staff members found to be guilty of misconduct will face severe action."
Moore leaves Tranmere following an 18-year association with the club as both a player and a manager.