Henin-Hardenne breezed through the first set in the indoor Schluefweg stadium but was made to fight for her second-round victory.
After holding on to win the second set tie-break 7-3, she said: "I knew she could come back because she is a fighter but I lost a bit of my aggressiveness.
"It is the end of the season and everyone is tired. I think I have played about 80 matches this year. My level is great but I have to take my time and I will have to be careful if I want to go further in this tournament."
The second seed will meet seventh seed Vera Zvonareva in the quarter-finals after the Russian beat American Amy Frazier 6-3 7-5.
Fourth-seeded Russian Elena Dementieva, the world number eight, lost to compatriot Nadia Petrova 7-6 6-3.
The two Russians broke each other three times in a hard-fought first set to take it to a tie-break which Petrova won 7-3.
"It was really pretty close,"
Petrova, who lost to Dementieva in the Filderstadt Grand Prix in Germany last week, dominated from then on as her opponent struggled with her serve.
"I was looking for revenge this time," said Petrova. "I had been looking forward to the match after last week's disappointment and after a very easy first match I was pretty confident."
Unseeded Jelena Dokic secured a place in the last eight with a 4-6 7-5 6-1 defeat of American Alexandra Stevenson and will play either third-seed Amelie Mauresmo or defending champion Patty Schnyder of Switzerland.
Dokic, beaten finalist here in 2001 but who lost to Stevenson in the second round last year, recovered from a set down to secure her first victory over the American on the indoor carpet surface.
"She started off well and I thought if I lose I won't be disappointed because she is playing well," said Dokic, who had not won two consecutive matches in 10 previous events.
"But it was just a matter of getting that one break, I think, and I got it at the right time to turn the match around."