New Ways Ministry pilgrims had attended events with Pope John Paul II and Pope Benedict in the past but never offered seats.
The group was not identified as being gay in the Vatican's list of attendees and identified only as a "group of lay people accompanied by a Sister of Loreto".
It was also not mentioned when a monsignor read out the different groups of pilgrims attending the audience.
Although the Pope did not acknowledge the group directly the Vatican would have had to directly reserved the tickets for the group.
New Ways Ministry officials said they were pleased they had been invited to sit with VIPs.