Flipkens has been in great form this week, beating Dominika Cibulkova and Mona Barthel - the first and third seeds - respectively en route to her first WTA Tour final.
She claimed the first set in dominant fashion against Hradecka but was made to work hard in the second before securing the all-important break in the 11th game and holding serve to seal a 6-1 7-5 triumph.
"I played really well and really aggressively in the first set," the Belgian told the WTA Tour's official website.
"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."
The defeat means Hradecka is yet to win a final in five attempts on the Tour, yet the Czech remains upbeat.
"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.