Undisputed champion Oleksandr Usyk vacated the belt on Tuesday and interim champion Dubois, 26, was elevated to champion status as a result.
Two-time world champion Joshua, 34, is on a four-fight winning streak and has three stoppages in his past three bouts.
Dubois has won his past two fights, stopping Jarrell Miller in December and Filip Hrgovic this month to become interim champion.
Ukrainian Usyk initially requested that he not be stripped of the IBF belt so the undisputed title could remain on the line when he faces Britain’s Tyson Fury in a rematch on 21 December, but then changed his mind.
“Anthony and Daniel, I know the IBF title is important to you. It is my present to you on 21 September,” Usyk said in a video message on X.
Dubois lost in controversial fashion to Usyk in August in his first bid to win a world title.
Dubois floored Usyk in the fifth round with what the referee deemed a low blow, before losing by stoppage in the ninth.
Dubois has won 21 of his 23 fights, while Joshua has 28 victories and three losses. They have a combined 45 knockouts.
It will be be the first time since Fury’s win over Dillian Whyte in December 2022 that Wembley will host boxing.
Joshua will be making his fourth appearance there – and third as a headliner – while Dubois will fight in a main event at a 60,000-plus venue for the first time.
The winner will put themselves in prime position to fight the winner of Usyk-Fury.
Analysis – big-time boxing returns to UK
BBC Sport journalist Kal Sajad
From Joe Bugner v Henry Cooper to Lennox Lewis v Frank Bruno, there is something a little bit special about an all-British heavyweight tussle.
This one is no different as it marks the return of big-time stadium showdowns to the UK.
Joshua will compete on home soil after his wins over Otto Wallin and Francis Ngannou in Saudi Arabia. Dubois’ previous two bouts were also in Riyadh.
There are few more experienced 26-year-old heavyweights than Dubois, and he has come a long way since a stoppage defeat in the 10th round at the hands of Joe Joyce in 2020.
Dubois battled unjust criticism afterwards as some labelled him a quitter, with doctors saying he could have lost his eyesight had the fight continued.
He might be a world champion for the first time, but his status as such will only be truly confirmed when he takes on Joshua.
The losses to Joyce and Usyk are firmly a thing of the past – Dubois is invigorated after the win over Hrgovic, despite being the underdog, and will feel he has the power to topple Joshua and become Britain’s poster boy of the division.
But Joshua is also enjoying a resurgence and, with three straight stoppage victories, the 2012 Olympic golden boy has gone some way to silencing his critics.