Henin, the top seed in 's-Hertogenbosch, the Netherlands, stormed back after dropping the first set -- the first time she had done so this week -- to collect her 43rd career title.
The former world No. 1 broke service twice in the second set and then spotted Petkovic a 3-0 lead in the decisive third. Henin was able to break back in the fifth game and racked up another break for a 5-4 lead before serving out the win.
With the win, Henin could be parlaying a strong season into a deep Wimbledon run. The last time she won in 's-Hertogenbosch in 2001 she followed by reaching the finals at the All-England Club.
Henin has returned this season after two-year absence to win in Stuttgart and reach the finals at Brisbane and the Australian Open. Wimbledon, however, remains the only Grand Slam event she has yet to win.
Petkovic was trying for her second career WTA title.