Andoni Zubizarreta has been sacked by Barcelona president Josep Maria Bartomeu and Carles Puyol quit soon after.
The sporting director, who took the role in 2010, had blamed Bartomeu for the FIFA transfer ban on Sunday night, although he may already have known his fate.
Zubizarreta has been widely criticised for bad signings like those of Thomas Vermaelen and Douglas last summer.
A Barcelona statement read: “The Barcelona president, Josep Maria Bartomeu, has decided to terminate 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.”
Puyol's resignation came around an hour later. He had been in an assistant role to Zubizarreta for around three months.
The former defender posted on Facebook: "With this statement, I want to announce I have decided to terminate my employment with Barcelona Football Club.
"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 want to experience other things form another perspective and from elsewhere.
"I want to grow both personally and professionally so that, in the future, hopefully I can return home and give you back everything you have given me during these unforgettable years.
"I remain extremely grateful to employees, directors, president and sports management for trusting me and helping me in this transition, which is not easy. And especially to the fans, as a player I have always felt very close to them, and now, since my retirement, I feel that even more.
"I wished to say goodbye to all with my boots on, but life is not always what you want. I have been and am very lucky to feel so much love, so I can only say THANK YOU and to know that I always carry it in my heart. Visca Barca."