Bartomeu's departure comes following mounting pressure from fans and his public falling out with Lionel Messi.
His resignation could even affect the future of Messi, who will now be given a new project after the Argentinian tried to leave in August, citing a lack of direction at the club.
"I want to communicate my resignation along with the rest of the board," said Bartomeu in a official announcement. "It's a composed and relaxed decision, agreed with all my fellow directors."
However, it was his revelation about a Super League which seems certain to make the biggest waves beyond Catalonia.
Bartomeu said he accepted a proposal on Monday for Barcelona to play in "a future European Super League" which "would guarantee the financial stability of the club".
An election for Bartomeu's successor will take place within the next three months, although it is expected to happen sooner, while an interim board will be put in charge in the meantime.
Bartomeu will go down as arguably the worst president in Barcelona's history. His six-year tenure saw a dramatic decline in the performances of the team and he oversaw Messi, the club's greatest ever player, trying to leave the club for free.