The National Party voted to oust former leader Michael McCormack and replace him with Joyce last week.
Keith Pitt will continue to as minister for resources and water, but will not be part of Cabinet.
That is despite new data today from the Office of the Chief Economist which predicts Australia's resource and energy exports will hit a record A$310 billion in 2020-21, with almost half of those earnings coming from iron ore alone.
In 2021-22, a further significant rise in exports to $334 billion is forecast, before moderating world economic growth and falling prices reduce exports to just below $304 billion in 2022-23.
Pitt also lost the Northern Australia portfolio to David Littleproud, with Susan McDonald to take on the role of envoy for Northern Australia.
"It's been a privilege to have served as a Cabinet minister. I look forward to continue working with the resources and water sectors that are both crucial to the national economy," Pitt tweeted.
The decision was slammed by many.
"The resources industry is the backbone of the Australian economy. But that isn't enough for the Morrison Joyce government to have the resources minister in Cabinet," shadow resources minister Madeleine King tweeted.
"The Liberals & Nationals take the resources industry for granted. Don't believe a thing they say."