Her riding career was threatened after she suffered serious injuries in a race fall in May previous year.
Racing Victoria said stewards received a report from Racing Analytical Services Limited confirming the presence of Phentermine, an appetite suppressant and banned substance in accordance with Australian Rule of Racing 81B, in the sample provided.
She has been stood down from riding in races and trackwork.
"I just couldn't believe we'd won the Melbourne Cup, it's a dream come true", the 30-year-old told ABC after her win.
The Herald Sun attempted to contact Payne on Wednesday night.
Jockeys who have been found guilty of this offence in the past, faced bans of one or two months. She is scheduled to return to England to ride Kaspersky later this summer, and to also compete in the Shergar Cup.
Earlier this year Payne took out a trainer's licence.