Puyol, 36, had to fight back tears as he declared to the press on May 15 that he had played his last game for the club after 593 appearances spanning a 15-year career.
"The appointment of Puyol means that one of the most emblematic captains in club history will be remaining at the club," Barcelona said in a statement.
Puyol said he would do his best in the new job.
"Now I need some time to rest and continue treatment on my knee, but I am really looking forward to it. I am very excited about this new stage of my life," he said in the club statement.
Puyol had said in March that he would rescind his playing contract at the end of the current campaign due to the knee injury, but hinted he could stay with the Catalans beyond the end of the season in a different capacity.
Barcelona said the former player would join the club's football department, assisting the sports management team.
"We will be seeking to exploit and learn from all of his experience," said Barcelona football director Andoni Zubizarreta.
"We will have him close to all the teams, it is a unique opportunity," Zubizarreta said in the statement.
"A couple of years ago we spoke about what would be best for him and I'm sure he will come to realise that is what he'll enjoy the most."
Zubizarreta said Puyol would work on club projects, including in areas such as marketing, finance and football player signings and transfers.