Hlavackova and Hradecka, who upset Serena and Venus Williams in the semi-finals, overcame a swift start from the Australians and finished strongly to claim their second major doubles title following their 2011 French Open triumph.
It was also a second title for Hlavackova at this year's US Open after she teamed up with Belarusian veteran Max Mirnyi to win the mixed doubles on Friday.
"It's been amazing," Hlavackova said. "I can't believe I have won two grand slams this week. "I want to thank Lucie. She helped me as much as Max did."
It was third-time unlucky for Barty and Dellacqua, who lost both of their previous grand slam finals at the Australian Open and Wimbledon this year.
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