Defending champion Patty Schnyder also reached the last eight by upsetting third seed Amelie Mauresmo 6-2, 6-2.
Clijsters took her tournament title tally this year to seven with victory in the Filderstadt Grand Prix in Germany last week and she is on course for second a consecutive final showdown with compatriot Justine Henin-Hardenne.
Srebotnik did little to stand in her way and, despite her plucky effort, collapsed to the all-round strength of the Belgian in front of an enthusiastic crowd at the indoor Schluefweg stadium.
"I knew she would be tough because she really likes to play aggressive tennis," said top-seed Clijsters, who lost her last match against Srebotnik in Los Angeles last year.
"I had to stop her playing her game and I played really well. I broke twice in each set but the games were close, especially in the beginning, and we had some really great fun rallies out there.
"I felt like she did not give me many easy mistakes and I had to work for it and make sure I was playing well enough. But it is good to win matches like that."
Clijsters, who had not played in four days after being given a bye in the opening round, started the stronger by securing a double break and comfortably held her serve to move into a 3-0 lead in the opening set.
Srebotnik, playing with strapping on her left thigh, won her first game of the match when Clijsters hit the ball wide.
She refused to roll over and took three points from Clijsters when 5-2 down, but squandered three break points and lost the set.
The second set started like the first, with Clijsters breaking twice and holding easily to move into a 4-0 lead.
Srebotnik managed to prevent a whitewash by winning two games but the match was all over in 57 minutes when the Slovenian hit the ball long.
Clijsters will next meet another Slovenian, the unseeded Tina Pisnik, who beat Japan's Ai Sugiyama, the sixth seed and world number 11; 5-7, 6-3, 6-3 on Thursday.
Swiss Schnyder lost to Frenchwoman Mauresmo in Filderstadt last week but she drew on the support of a 5,635-strong crowd to turn that result around on home soil.
The local favourite broke Mauresmo's serve in the first game and again in the seventh before serving out the set.
She then raced into a 4-0 lead in the second set and held her form to set up a clash with Yugoslav Jelena Dokic.
