The 36-year-old Mirnyi's hat trick of wins in the event, each with different partners, was completed 15 years after his first at Flushing Meadows and was the 10th major doubles title of his career.
He partnered with Serena Williams to win the US Open mixed doubles crown in 1998 and then triumphed with Victoria Azarenka in 2007.
Mirnyi's successes in the format also includes a mixed doubles Olympic gold medal that he won with Azarenka in London last year.
"Max was unbelievable, he covered 80 percent of the court and made it easy for me to make some great returns," said Hlavackova.
Hlavackova is back on court later on Friday in the women's doubles semi-finals where she and fellow Czech Lucie Hradecka face the Williams sisters.