Zubizarreta, who kept goal for Barcelona between 1986 and 1994, returned to the club in July 2010 to take up the role from which he has now been fired.
A club statement read: "The FC Barcelona President Josep Maria Bartomeu has decided to terminate as of today the contract of the club’s director of football, Andoni Zubizarreta.
"The president, in the name of the club, thanks Andoni Zubizarreta for his contribution, dedication and professionalism over the last four years in his role at the head of the club’s football area."
Within hours, Puyol - who had been assisting Zubizarreta since retiring as a player last year - announced on Facebook that he has resigned.
His statement read: "I want to announce that I have decided to end my employment with Football Club Barcelona. These three-and-a-half months have given me the opportunity to see the other side of the club. I learned a lot, I’m very grateful and now I would like to experience other things from another perspective and elsewhere.
"I want to grow both personally and professionally so that, in the future, hopefully someday I can return and give back everything you have given me during these unforgettable years. I remain extremely grateful to my employees, directors, president and sporting team for trusting me and helping me in this transition, it has not been easy. And especially to the fans.
Tenant du titre avec l'Espagne, Carles Puyol a amené le trophée sur la pelouse du Maracana avant la finale Allemagne - Argentine.
Image credit: AFP
"As a player I always felt very close but now, after my retirement, I feel even closer. I wanted to say goodbye with my boots on, but life is not always how you want it to be. I have been, and still am, very lucky to feel so much love, so I can only say THANK YOU and to know that I always carry you in my heart. Long live Barca”.
Spanish daily Marca reported three days ago that Zubizarreta's days were numbered at Camp Nou after president Bartomeu lost faith in his abilities and started the search for a replacement.
Barcelona's transfer ban for 2015 could be seen as a contributing factor, but concerns over the squad built by Barca and the quality of some recent signings have also been cited as reasons for Bartomeu's decision to wield the axe.
FC Barcelona Sport Director Andoni Zubizarreta and Luis Suarez of FC Barcelona pose for the media
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Marca highlighted Zubizarreta's failure to solve the club's impending right-back problem with Dani Alves possibly leaving the club and replacement Douglas looking unconvincing - while the fact that summer signing Thomas Vermaelen hasn't played a game due to long-term injury has also been held against the former keeper.
On Sunday Zubizarreta had spoke out about the transfer ban, which was imposed for breaching rules on the signing of youth players: "As the director of football, I assume full accountability for my responsibilities. Mr Bartomeu is the one who knows the situation better than anyone, as he was the sporting vice-president during that time. My position is always the club’s decision."
Thomas Vermaelen and Luis Suarez of FC Barcelona shares a joke during the official presentation of the FC Barcelona prior to the Joan Gamper Trophy match
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THE VIEW FROM SPAIN - A TACTICAL MOVE BY BARTOMEU
Adrian Garcia, Eurosport Spain: "In Zubizarreta's interview yesterday he spoke against president Bartomeu, regarding the FIFA ban. In our opinion, sacking him is a strategic move by president Bartomeu. He could save his presidency with this decision. Bad transfers are another issue, especially Vermaelen this season."