This version features a newly written chorus by Reuben Morgan and Ben Fielding.
Twenty-two people died in the floods, Queensland's worst natural disaster. Flood waters have also affected the state of Victoria.
All the proceeds from sales will go to the Queensland Premier's Disaster Relief Appeal, set up to support the tens of thousands of people affected.
Hillsong Australia has already been meeting the needs of those affected in the last few weeks in a coordinated response with Australian Christian Churches.
Hillsong's Brisbane campus was registered as one of the city's official evacuation centres, while church members opened up their homes to other church members in need of a place to stay.
The church has also collected food and cleaning products at its Sunday services and signed up volunteers to help in the clean up operation.
The single and free sheet music are available to download at hillsongmusic.com/categories/live/itiswellwithmysoul