The former Subaru works driver has started two events this year: Rally Mexico with the Monster Ford team and Rally Finland in a Citroen DS3.
Araujo was expected to stay with the team all season, but the squad said it wanted to give him a break to "regain his focus".
"After our Rally Finland debrief and further conversations with Armindo since returning home, we decided that it was better for him to take a break, relax and regain his focus on the sport and how he approaches it," said team manager Bruno di Pianto.
"The decision was not taken lightly and was made on purely sporting grounds. It was not a personal decision and everyone in the team wishes Armindo all the best for the future."
Atkinson becomes the team's number one driver and he will be at the wheel of the factory-supported Mini WRC starting in Germany next weekend.
"Mini has provided me with an awesome opportunity to return to the world championship and I'm stoked to be back as a lead driver for a great manufacturer and for the remainder of the 2012 season," said the Australian, who is yet to drive the car.
"I love the Tarmac so it's great to know that three of the remaining five events are on the sealed surface, and I hope to take full advantage of my past experiences of the remaining rallies this year."
- Rally Mexico