Laughing and smiling, the monarch waved off Higgins at Windsor Castle, west of London, after a four-day trip that both countries hope underlines the new strength of their relations.
The president earlier hailed his "memorable" state visit, the first by an Irish president since independence from Britain in 1922, as "so positive, so uplifting and so hopeful".
Higgins claimed the visit showed both countries had come to terms with their painful history, and both he and the queen celebrated the hard-won peace in Northern Ireland, which remains part of the United Kingdom.
Former Conservative minister Norman Tebbit said he hoped one of McGuinness's former IRA colleagues "might shoot him in the back" for "bowing to the queen".
Tebbit, who was injured during an IRA bombing in Brighton in 1984 which targeted a Conservative Party conference, later withdrew the comments, saying they were not meant to be taken literally.
Higgins's visit came three years after the queen made a ground-breaking first trip to the republic, which helped to heal deep-rooted unease and put British-Irish relations on a new footing.
He was treated to a brief performance from "Henry IV" and took to the stage himself at the Royal Shakespeare Theatre.
"The words exchanged between Ireland and England have often been part of a long and sometimes tortured exchange," he said.
"If it was once the forced language of conquest, it is today the very language in which we have now come to delight and share."
He spoke of "the present happy face of relations between our two people as we pass slowly but surely into a new kind of relationship".
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