Naitanui, whose start to the year has been delayed following off-season groin surgery, has been locked into the Eagles' 22 to play the Western Bulldogs at Patersons Stadium.
And Waite, who has been gaining match fitness in the reserves following a calf injury, adds a tall forward target for the Blues in Sunday's clash with Melbourne at the MCG.
Forward Sam Rowe has been omitted to make way.
The Demons have made six changes through injury and omission, with young midfielder Jack Viney among them as he returns to the side from a week's rest.
Former Collingwood midfielder Sharrod Wellingham has also been selected in West Coast's final 22 to make his Eagles debut after a trampoline accident delayed his season start.
Earlier on Friday, Paul Chapman was a late withdrawal from Geelong's blockbuster clash with Richmond at the MCG.
The Cats veteran had been due to return against the Tigers on Saturday night after missing last week's win over the Western Bulldogs with a hamstring complaint and is still suffering from soreness.
Chapman has been replaced in the Geelong side by pacy youngster Jordan Murdoch.
Josh Caddy, who was omitted this week, has now been named an emergency for the Cats.
Click here for the full round six teams, including Sunday's line-ups
