Cricket Australia said Lee, 35, suffered the fracture after he was struck by a ball in his last over against India in Friday's Twenty20 international at the Melbourne Cricket Ground.
Team doctor Trefor James said Lee, who has made 205 ODI appearances, will be out of cricket for up to six weeks.
"Brett Lee sustained a fracture of his right foot when he was struck by a ball in his last over of the T20 match on Friday," James said in a statement.
"He was able to complete the over however the foot became more painful and swollen the following day.
"An X-ray has confirmed a fracture of the small toe and we now expect Brett will return to cricket in four-six weeks."
CA said a decision regarding a replacement player for Lee would be made after Sunday's opening ODI against India at the MCG.
