The Presidency announced Nene would now be deployed to what it calls a strategic post.
Last week, Nene told South African Airways (SAA) Chairman Dudu Myeni she should not go ahead with a planned new deal with Airbus.
Myeni is also the chair of the Jacob Zuma Foundation.
Former Merafong Mayor David van Rooyen is the new finance minister.
But Nomura economist Peter Attard Montalto says that the timing of Nene’s firing is very odd.