Zubizarreta's dismissal follows Sunday's disappointing 1-0 La Liga defeat to Real Sociedad and the news last Tuesday that the club had lost its appeal to the Court of Arbitration of Sport (CAS)
following the decision to ban it from being able to sign new players over the next 12 months.
A former goalkeeper for the club, Zubizarreta had been responsible for Barcelona's transfer business since returning to the Camp Nou in July 2010.
"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," an official Barcelona statement read
"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."
Zubizaretta wasn't the only leading figure at Barcelona to leave the club Monday after Puyol confirmed on his Facebook page
that he would also be departing.
A former captain of the club, who won three Champions League crowns and six La Liga titles, Puyol was appointed assistant sporting director soon after retiring as a player in May.
"These last three months gave me the opportunity to see the other side of the club. I learned a lot, I am very grateful and, now, I want to try other things from another perspective and in other places," Puyol wrote.
"I want to grow both personally and professionally so that, in the future, I can return to this home and give back all that you gave me during these unforgettable years.
"I remain extremely grateful to the employees, directors, president and sports management for trusting me and for helping me in this transition that was not easy.
"And most of all to the fans who, if I felt they were supportive when I played, now, since my retirement, I feel that even more.
"I wish I could have said good bye to everyone with my boots on, but life does not always goes as one desires. I have been and I am very fortunate too feel as much love and support, for which I can only say THANK YOU and let you know that I will always carry you in my heart.
"Long live BARCA."
CAS's decision, which found Barcelona guilty of breaching FIFA rules on signing minors, means the club is unable to add to its squad during the next two transfer windows. The Spanish club, also hit with a $455,000 fine, says the transfer ban is "disproportionate" and "excessive."
After Barcelona's loss to Real Sociedad -- a result which meant it missed the chance to move top of the La Liga table -- Zubizarreta suggested in an interview with Canal+ that he was not solely to blame for the transfer ban.
"Taking responsibility is to explain the actions, how the decisions were made, but I have little to explain because the vice-president [Bartomeu] who was in charge of that area [at the time] is the current president," he said.
FIFA first issued the ban in April
, but with Barcelona appealing the decision it was free to buy players until that appeal was then rejected by world football's governing body in August.
Zubizarreta helped to bring Luis Suarez to the club from Liverpool in the summer, which was met with much excitement from supporters, yet other signings have not been met with such acclaim.
Douglas was signed from Sao Paulo but has only made three appearances this season, while Thomas Vermaelen has yet to make his debut for the club since joining from Arsenal due to injury.
Zubizarreta also helped sign the likes of Adriano, Javier Mascherano, Alexis Sanchez, Cesc Fabregas and Neymar, who have all proved relative successes.
Zubizarreta played for Barcelona between 1986 and 1994, helping the side to a first ever European Cup in 1992.
The Spanish club is yet to announce who will fill the vacancy left by the 53-year-old.