It was 1-0 to the visitors after just two minutes at the Amex Elite Performance Centre when Tyler Hamilton crossed for Ben Hinchcliffe to tap in.
Aaron Connolly levelled for the Seagulls on 27 minutes with a fine finish.
Four minutes before half-time, Tom Powell put Hull back in front.
Sam Baldock tapped in on 56 minutes to make it 2-2 before Hull's Lewis Ritson was sent off for a professional foul.
Tom McGill could only parry Lewis-Potter's header and the 16-year-old reacted to poke in the winner.
Brighton remain top of the group while Hull are third after their first win.
See: Brighton report
Brighton: 18 Nov v Stoke City (H) PL2
Hull: 30 Nov v Sunderland (H) PL Cup
(Photo courtesy of Brighton & Hove Albion FC)