Webb, 43, started his refereeing career in 1989 and oversaw his first Premier League match in October 2003, before being added to Fifa's international referees' list two years later.
In 2010, he took charge of the Champions League final between Inter and Bayern Munich and then the World Cup final in South Africa as Spain beat Netherlands, where midfielder Nigel de Jong escaped punishment for a lunging high challenge on Xabi Alonso before Johnny Heitinga was sent off.
Webb also took part in the finals in Brazil this summer, where he took charge of the hosts' last-16 clash with Chile in Belo Horizonte.
Webb's new role will include "overseeing the technical direction and standards that govern the on-field performance of PGMOL's match officials", according to an official statement.
He will also be responsible for the training and coaching of referees, as well as "informing and educating" the public on refereeing issues.
"I am very excited to start this new chapter in my career after a wonderfully rewarding 25 years on the pitch," Webb said.
"I have spent over a decade with the best seat in the house for Barclays Premier League matches, been lucky enough to be involved in nine major international tournaments, and taken charge of the Uefa Champions League and Fifa World Cup Finals.
"Refereeing has given me so much and I think it's important that match officials who have had the rewards remain in the game to pass on their knowledge.
"I also have much more to learn about the business of refereeing and I believe the best place for me to do that is with PGMOL. It's an incredibly positive working environment and we all have a common goal of improving refereeing.
"Over the last five years in particular we have made huge strides in terms of our accuracy, fitness and professionalism. The current Select Group are the best referees this country has ever produced and I am thrilled that I not only get the chance to continue working with them but also the opportunity to help develop the next generation of Select Group officials."
Mike Riley, former Premier League referee and general manager at PGMOL, added: "Howard has been the foremost referee of his generation and an inspiration for match officials in this country and around the world."