Ayto replaces David Weir after the Scot's departure last week.
Formerly working alongside Edu at Arsenal, Ayto takes charge with immediate effect and said: “I’m honoured to be appointed sporting director at Brighton & Hove Albion and I’m very grateful to Tony Bloom, Paul Barber and the board for this opportunity.
“This is a special club, admired across the footballing world for its culture, ambition and smart thinking, all of which has underpinned some remarkable progress in recent years.
“To be joining at a time when there is such a strong desire to build on those excellent foundations, innovate further and bring success is incredibly exciting.
“I’m looking forward to getting started and working with, and supporting both our head coaches Fabian Hurzeler and Dario Vidosic, and their respective playing squads.”
Mike Cave, meanwhile, has been named new technical director at Brighton.