Poyet has been linked with a possible move to Spurs to become the assistant manager to Juande Ramos, who is tipped to replace Martin Jol.
Despite Leeds insisting no approach has been made for Poyet, it has now been agreed that he will miss the Millwall fixture.
The Whites have confirmed experienced midfielder Alan Thompson, who is currently out injured, will assist manager Dennis Wise.
Leeds' statement - released before they announced Poyet would miss Saturday's match - read: "Despite the widespread speculation that has emerged linking Gus Poyet with a potential role at Tottenham Hotspur within a new management team following the departure of Martin Jol, Leeds United can officially confirm we have neither received an approach from Tottenham for Poyet nor a request from him to be released from his contract with Leeds.
"Any approach from Tottenham for our assistant manager would not be welcome."