It costs 2,318 Canadian dollars a night including taxes, or almost NZ$2600.
One of the smaller suites would be 1,854 Canadian dollars (NZ$2151).
Although she was born in the US, Miss Markle has lived in Toronto, where she films the legal drama Suits, for five years.
When he visits his girlfriend in the city, Harry, 33, normally stays at her rented house in a quiet, upmarket suburb.
Cars being used by his security detail were spotted at the low-key residence when he arrived in Canada last week, several days before the start of the Invictus Games, the sporting competition Harry created for injured servicemen.
Since then, the couple have moved to downtown Toronto, where they have been discreetly living together at the Fairmont.
The hotel, which opened in 1929, recently completed a five-year multi-million-pound refurbishment. A source said Harry needs to be in the city centre for engagements and meetings and was also concerned about the presence of photographers outside Miss Markle's house.
They added: "Why wouldn't he want her to stay with him? They live apart so much as it is."
Harry and Meghan, 36, who have been dating for 14 months, made their first official appearance together as a couple on Monday when they attended a wheelchair tennis match.
They arrived and left holding hands, and spent half an hour in full public view, cheering the competitors and laughing together.
Miss Markle, who wore a white Misha Nonoo shirt called The Husband, ripped jeans and flat shoes, appeared unconcerned by the attention as she sat at her boyfriend's side.
Their willingness to be seen - and photographed - together is being seen as a further sign that the couple are heading towards marriage. Harry is said to be besotted with divorcee Miss Markle, and it is understood she is making plans to move to London to be with him permanently.
On Saturday, Miss Markle had joined Harry at the opening of the Invictus Games. She was discreetly chaperoned not only by one of Harry's Scotland Yard police protection officers but also by Rose Hall, of the Invictus Games Foundation, who has spent the week by Harry's side.
Miss Hall, who provides Harry with guidance and support at Invictus events, had apparently been placed in front of Miss Markle in case she needed assistance.
Back in the UK, Prince William gave a diplomatic laugh yesterday when asked about the prospect of his younger brother getting engaged. William was on a day of engagements in Milton Keynes to mark the 50th anniversary of the town, when he visited William Cowley Parchment and Vellum.
Paul Wright, the firm's general manager, told him: "If Prince Harry marries Meghan then his certificate will be in our vellum."
Royals can marry only if the Queen gives her formal blessing on a calf-skin document called the instrument of consent. Mr Wright said afterwards: "He just laughed a nice laugh."
The process takes six weeks, and if Miss Markle and Harry do tie the knot, their instrument of consent will be made by master vellum maker Lee Mapley, 37.
