It was the first time the IOC has honoured the slain Israelis in a ceremony inside an Olympic village.
Rogge has repeatedly rebuffed calls to hold a moment of silence during Friday's opening ceremony of the London Games. He said Saturday the opening was not the appropriate place to remember the Israeli team members killed by Palestinian gunmen at the 1972 Munich Olympics.
On Monday, Rogge chose a different venue and occasion to hold a special observance.
"I would like to start today's ceremony by honouring the memory of the 11 Israeli Olympians who shared the ideals that have brought us together in this beautiful Olympic Village," Rogge said. "The 11 victims of the Munich tragedy believed in that vision.
"They came to Munich in the spirit of peace and solidarity. We owe it to them to keep the spirit alive and to remember them."
Rogge bowed his head as a crowd of about 100 people — IOC executive board members, dignitaries and Olympic athletes and officials — stood in silence for a minute.
"As the events of 40 years ago remind us, sport is not immune from and cannot cure all the ills of the world," Rogge said.
Rogge spoke from an outdoor stage during a ceremony promoting the Olympic Truce, a U.N.-backed initiative calling on warring parties around the world to end hostilities during the period of the games. Rogge and other officials signed the "truce wall" after the event.
Rogge and the International Olympic Committee have come under pressure from Jewish groups and politicians in the United States, Israel and Germany to honour the Munich victims during the opening ceremony.
"We feel that the opening ceremony is an atmosphere that is not fit to remember such a tragic incident," Rogge said Saturday.
Rogge and the IOC will also honour the slain Israelis at a private reception in London during the games on Aug. 6. The IOC will also take part in a ceremony in Germany on the anniversary of the attack on Sept. 5 at the military airfield of Furstenfeldbruck where most of the Israelis died.
During the second week of the Munich Games, eight members of the Black September militant group penetrated the laxly secured Olympic Village and took Israeli team members hostage. A day later, all 11 were dead. German police killed five of the eight assassins during a failed rescue attempt.
Still, Monday's tribute did not fully satisfy families and advocates for the victims.
Ankie Spitzer, whose husband Andre coached the Israel fencing team in 1972, said in a statement that Rogge's "private moment" was just a "rehearsal" for what they expected of him on Friday.
"We will continue our efforts to have the memory of our loved ones honoured at the opening ceremony," said Spitzer, who will speak at a news conference on Wednesday in London.
The United States-based Anti-Defamation League criticized the IOC for an "irrational and stubborn" refusal to honour those who died.
"This four-decade refusal to mark one of the most infamous terrorist attacks in history, and an attack on the Olympics Games themselves, represents a continuing stubborn insensitivity and callousness to the memory of the murdered Israeli athletes," Abraham H. Foxman, the ADL's national director, said in a statement.
Rogge, who competed in sailing at the Munich Games, said Monday's tribute was heartfelt and not a response to the demands for a commemoration during the opening ceremony.
"It has nothing to do with the requests," he said. "It was a spontaneous gesture from me because we are here in the Olympic Village where the athletes were killed, part of them at least. This is a place where we speak about sport and peace. It's absolutely normal I should call for a remembrance of the Israeli athletes.
"I couldn't speak here in front of the athletes and the national Olympic committees about peace and sport and about the Olympic Truce without remembering or reminding the people what happened 40 years ago and the disaster that also started in the Olympic Village in Munich, so it was fitting that I would say what I feel about that."
The remembrance came at the end of a tour of the village by Rogge and the executive board. Rogge inspected a room in the Brazilian housing area, watched a team-welcoming ceremony featuring circus performers, chatted with British volleyball player Nathan French in the game room and sat in the cafeteria with Australian athletes who greeted him with "G'day mate."
Rogge, who is attending his 21st Olympics, had rave reviews for the facilities.
"It's a Premier League Olympic Village," he said.
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