Flipkens, 26, dominated the first set and managed to grind out a tough second with a break in the penultimate game, adding Czech eighth seed Hradecka to an impressive week’s work which saw her oust top seed Dominika Cibulkova.
"I played really well and really aggressively in the first set," Flipkens said. "I feel my only advantage in the second set was the break at 5-5 - it was a really close match and I was down in a lot of the games I won.
"I have to give credit to her - she came back strong in the second set."
World number 50 Hradecka, 27, has now lost all five of her WTA Tour finals.
"I didn't start well. But all credit to her. It's tough to lose in a final again, but hopefully I can win my next one," she said.