On a day of upsets, Henin suffered a shock third round exit at the hands of Russian Dinara Safina, while third seeded Russian Svetlana Kuznetsova also crashed out after her third round defeat to Ukrainian Alona Bondarenko.
Williams had few problems in her third round 6-3, 6-1 win over Agnieszka Radwanska, her 17th straight victory after winning the Miami, Charleston and Bangalore WTA tournaments this year. But she said her number of wins was irrelevant and she was just happy not to suffer the same fate as Henin, who was earlier beaten 5-7, 6-3, 6-1 - her second defeat in her last three games.
"Yes, that was my 17th win on the trot, but I am not even keeping count, it's just about winning these games every day," said fifth-seed Williams. "You can never under-estimate these Tier I tournaments, every day is a battle out there."
Williams, who hammered Henin 6-2, 6-0 in Miami at the start of last month, now plays Safina in the last eight, but said world number one Henin is more than capable of bouncing back after her latest setback.
"I am surprised she lost, she is a good winner and people have a lot of expectations of her," said Williams. "She will play a lot better and this is just one tournament."
Against Safina, Henin fought back from 4-2 down to win the first set 7-5, but the Belgian lost the second set 6-3. Safina had five match points in the third set at the end of the two hours 34 minute marathon and broke the Belgian eight times in total as Henin's poor run continues this season.
"It was pretty difficult out there and very frustrating, I am very disappointed," said Henin. "I struggled during the whole match, I didn't have the intensity or the stability, she just played better then me."
Having won the last three French Open tournaments, this was not the ending Henin wanted in Berlin and she has just next week's WTA event in Rome to prepare before Roland Garros begins in Paris on May 26.
"This week was important, not only in terms of the French Open, but also in terms of getting some confidence back," said Henin, the top seed in Berlin. "I will take a few days off, focus on Rome and we will see what happens now in the next few weeks."
Having been beaten in all of her five previous matches against Henin, Safina was delighted with the win. "It's the biggest win of my career so far, after losing all of my five games to her it was a long time coming," she said.
Earlier in the day, last year's finalist Kuznetsova was humbled 1-6, 6-2, 6-2 by 15th seed Bondarenko.
There were no such problems for seventh seeded Russian Elena Dementieva as she saw off compatriot Vera Dushevina 7-5, 6-3 to make the quarterfinals. Dementieva will play fourth-seed Jelena Jankovic in the last eight after the Serb's 6-2, 6-4 win over Russian Maria Kirilenko.