Stubbs managed to win just one game in his five month spell at the Millers and the south Yorkshire club has decided to act in order to try to preserve the club's Champinship status.
The club said in an official statement: "Following a board meeting this morning it was felt that a change of first team management was needed to give the club the best possible opportunity to preserve our Championship status.
"The club would like to place on record our thanks to Alan, John and Andy for their effort and professionalism, and we wish them well for the future.
"The board have now started the process of appointing a new first team manager".
Former Wolves and Milwall manager Kenny Jackett is currently the favourite to succeed Stubbs.