She was pictured having a face-to-face audience with Gen Sir Nick Carter, chief of the defence staff, at Windsor Castle.
The monarch, 95, made the decision to miss Sunday’s event “with great regret”, Buckingham Palace said.
The palace had previously said it was the Queen’s “firm intention” to attend.
She had been taking time away from her duties for health reasons, having been advised by doctors to rest until mid-November.