Barcelona had wanted to suspend today’s game with Las Palmas as the Catalan public vote on independence.
A supporters group had threatened to invade the pitch in protest over police treatment of voters, with violence being sparked across the region.
Eventually it was agreed that the match would be played behind closed doors after La Liga threatened a six-point sanction if Barca refused to stage the game.
Vice-president Carles Vilarrubi resigned shortly after a Barca statement confirming the game would go ahead.
And Mones has now joined his colleague in exiting the Nou Camp.
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Mones was in charge of Barca’s medical set-up.
He was an advocate of the Catalonia independence referendum but was also keen for Barcelona not to dispute security forces who has made assurances the game would be safely policed.
Once Barca’s board discussed whether or not to suspend the game, Mones saw it as a matter of principle to step down, claim Spanish newspaper Mundo Deportivo.
Barca eventually won the game 3-0 with two goals from Lionel Messi and a Sergio Busquets header.