"She has gone down, she will go down as one of the greatest to grace the Australian turf," Bowman said.
"She would have before today but it has so much meaning to everyone in our industry."
Starting a prohibitive favourite at $1.15 Winx held off Humidor to win by a long neck with Godolphin's English-trained Folkswood third.
Bowman said former Kiwi trainer Chris Waller deserved all the credit for guiding Winx on career that has netted an Australian record 15 group one wins.
"To be able to manage an animal like this and bring her back three years in a row to peak on one particular day, I think it goes unnoticed," he said.
And while it's hard to imagine there is a more popular horse in Chris Waller's stable than Winx, Who Shot Thebarman is right up there.
The nine-year-old cemented a place in his fourth Melbourne Cup with victory in the Moonee Valley Cup (2500m) over his stablemate Libran who also heads to Flemington.
"In the stable he's just as popular as Winx," Waller said.
"He means so much to the staff and it shows if you look after them they will perform for you. He will run in in the Melbourne Cup for a fourth time.
"The first time he ran third. The second time he was knocked over and almost fell. The third time he ran fifth."
Who Shot Thebarman settled second last of the seven runners in the Cup (2500m) and came home strongly to beat Libran by a half head with the same margin to Cismonte.