Opener Watson and fast bowler Lee are both struggling with calf injuries they sustained in the eight-wicket defeat at Chester-le-Street on Saturday and will fly home for further assessment.
Australia team doctor John Orchard said in a statement: "Shane Watson and Brett Lee have calf strains - Shane to the left and Brett to the right calf - sustained during the fourth ODI against England at Durham.
"Because both players will miss the final game, they are flying back to Sydney for MRI scans and further treatment."
The statement continued: "At this stage, they are anticipated to be available for consideration for selection for the ICC World Twenty20, with scan results and response to treatment to determine whether they will be available for consideration for selection for the coming series against Pakistan in the UAE."
Mitchell Starc has been called up by Australia as cover for the injured pair.
England lead the series 3-0 ahead of the final one-day international at Old Trafford.