The Ralph Beckett-trained Cubanita collared Sajjhaa in the dying strides to claim the Betfred EBF Gillies Fillies' Stakes at Doncaster.
Dropping from Group One to Listed level, Godolphin's highly-rated Sajjhaa was sent off the 7-4 favourite and looked to have sealed it when Mickael Barzalona swept to the front approaching the two-furlong pole.
But her stride was shortening just as Cubanita's abundant stamina was kicking in entering the distance, and Jim Crowley's mount (8-1) was half a length to the good as they flashed past the line.
The lightly-raced maiden winner Reckoning ran on encouragingly to fill the places under champion jockey Richard Hughes.
Crowley said: "It's been stop-start with her this season so hopefully she'll stay in training next year, fingers crossed. I got a good trip round. They went a good gallop and everything went well in the end. I think she'll get a mile and a half. The last furlong was her best furlong."
Godolphin clinched the owners' championship with a double through Mar Mar and Muharrib, both trained by Saeed bin Suroor.
Mar Mar (7-2) showed a neat turn of foot two furlongs out to easily win the Betfred Cock O'The North EBF Maiden Stakes by four lengths under William Buick.
"She's a very honest filly, but she was a bit unsettled and keen last time, so we thought visors would help. She'll be a nice seven-furlong filly for next year," said Godolphin's representative Diana Cooper.
Muharrib (5-1) led over a furlong out under Barzalona to defy top weight in the Betfred 'The Home Of Goals Galore' Nursery.
Cooper said: "He's a very bonny horse who has thrived all season. He'll have a nice holiday now and he's one to look forward to. He's very honest and game and gives his all every time."
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