The band formed after the musicians met as students at Regent Street Polytechnic in the 1960s, and they returned to their alma mater, which is now part of the University of Westminster, to receive a permanent tribute.
The stars, who studied at the college along with late bandmate Richard Wright, unveiled a plaque dedicated to the band, and Waters said of the achievement, "We are hugely gratified to be here and to have the plaque. It's an honour."
Wright, who died in 2008, was represented at the event by his first wife Juliette Gale, who also studied at the college.
She added, "I was at the Poly (college) too and it's lovely to be back. Quite nostalgic actually as it seems like a long time ago. Having a plaque is a lovely thing and it's nice that Richard can be remembered by it."
Geoff Petts, Vice Chancellor of the University of Westminster, said of the Pink Floyd honour, "The University of Westminster is always proud to pay tribute to the achievements of our alumni. We are delighted to be associated with the global success of Pink Floyd and celebrate that today with the unveiling of this plaque."