After trading the first two sets Saturday, Petkovic broke the top-seeded Belgian in the second game of the final set before holding serve for a comfortable 3-0 lead.
But Henin held serve and blasted a forehand winner on her way to breaking the German in the fifth game. Henin, who did not drop a set or face a tiebreak heading into the final, completed a stunning rally by breaking Petkovic in the ninth game.
Stakhovsky unsettled Tipsarevic with a slicing backhand and precise net play on Saturday to win his third ATP title. The match lasted only 55 minutes on Saturday.
The unseeded Ukrainian had previously won titles in Zagreb in 2008 and St. Petersburg last year.