Lee was unable to complete his 10-over spell during the first ODI in Baroda and was not available for selection in following matches in Nagpur and Delhi.
'Brett's elbow injury has not responded as well to treatment as we would have liked and, therefore, a verdict has been made to send him home to consult with an elbow specialist,' CA physiotherapist Kevin Sims said.
'With an exact diagnosis, we can determine how best to manage the injury and give Brett the best chance of being available for selection at the beginning of the Australian summer,' he added.
Lee's mystery elbow injury also threatens to derail his Test comeback hopes. The timing could not be worse for veteran Lee - trying to convince selectors of his durability as he strives to again be Australia's Test spearhead this summer and take 400 Test and one-day wickets.
Lee's absence will also be a big blow for the Australian team. Captain Ricky Ponting admitted that Lee's absence at the death overs did make a difference as India pillaged 108 runs in the last 10 overs in Nagpur.
'Injuries cost a little more than expected at Nagpur. That's bit of a concern for us (bowling at the death). Brett is one guy who bowls well at the death and he has been doing a good job for us. But it depends whom you are bowling at. If there is somebody like (Mahendra Singh) Dhoni then you will go for some more runs in the end and that's what happened in Nagpur. He was well supported by Raina,' Ponting said.