It is Waller's first win in the Cox Plate, as it is for leading Sydney jockey Hugh Bowman.
"To be here riding on this stage is one thing. But to win a race like this, I can't tell you how much it means," Bowman said.
"I'm so thankful, obviously, to Chris Waller and the connections of the horse. I just can't believe it to be honest."
Winx settled in sixth position on the rail and when the leader The Cleaner shifted out, Bowman drove the mare through a narrow gap and she straightened with a winning break.
"At the 600 (metres), when The Cleaner rolled off and I went through I didn't want to be going that early," Bowman said.
Meanwhile David Hayes says the Owen Glenn-owned Criterion has produced an outstanding Melbourne Cup trial with his second placing in the Cox Plate.
Criterion finished a 4-3/4 length second behind Winx yesterday.
It was Criterion's second run in Australia after racing in Hong Kong and Europe following his victory in the Queen Elizabeth Stakes at Randwick in the autumn.
A plan was hatched in England to target the Cox Plate and Melbourne Cup with Criterion and the five-year-old showed he had returned from the United Kingdom in good order with his Caulfield Stakes success and yesterday's performance has done nothing to change Hayes' mind. "I reckon it was a really good Melbourne Cup trial," Hayes said.