The Welshman will oversee player recruitment at the Stadium of Light - and a domestic and international scouting operation - having left the Bundesliga giants.
Congerton told the Black Cats' official website: "I'm delighted to join Sunderland AFC and would like to thank the board and owner for this great opportunity.
"Working alongside (manager) Gus Poyet and his team was one of the influential factors in me joining the club and something that I am very much looking forward to."
Poyet added: "I would like to welcome Lee to the club. Recruitment is one of the most important areas in football nowadays, so I'm looking forward to working alongside Lee for the best of the club."
Congerton took up his role at Hamburg in 2011 having previously been employed by Chelsea as their chief scout.