Clijsters won the Brisbane title in 2010 and, after missing the 2011 edition, now has an 8-0 record in the Australian Open tuneup.
She raced to a 5-0 lead before Benesova, who ousted US Open champion Sam Stosur in the second round, launched a comeback with a run of three straight games.
Benesova held her opening serve and had an early break-point chance in the second set before Clijsters shifted up a gear and dominated the remainder of the match to earn a semifinal meeting against Daniela Hantuchova, who got a walkover in the quarterfinals when 13-time Grand Slam winner Serena Williams withdrew from the tournament on Wednesday after injuring her left ankle.
Clijsters had a tough three-set win over Ana Ivanovic in the second round but didn't let Benesova get too close in the quarterfinals.
"I'm very satisfied with the way that I played," Clijsters said. "In my previous match I lost my focus a bit. I was really focussed on not letting that happen today." Third-seeded Francesca Schiavone will meet Kaia Kanepi of Estonia in the other women's semifinal.
Schiavone saved two match points before coming back for a 5-7, 7-6 (2), 6-3 win over former No. 1 Jelena Jankovic.
The 2010 French Open winner saved match points on her serve in the 12th game of the second set and then, after winning the tiebreaker and going down a break in the third set, won the last five games to clinch a quarterfinal berth in just under three hours on her third match point.
Kanepi needed five match points to finish off a 6-1, 7-6 (7) win over second-seeded Andrea Petkovic.
"I just played really bad in the first set," Petkovic said. "My footwork was very sloppy, and afterwards I started moving a little better, but when somebody is hitting as hard as Kaia — and she was serving incredible — then you really have to be on point with your footwork.
"She played really, really well and I have to say, if she keeps playing like this she'll be a force." In the men's draw, second-seeded Gilles Simon of France advanced with a 7-6 (2), 6-4 win over Santiago Giraldo of Colombia. Simon will next play third-seeded Alexandr Dolgopolov, who rallied to beat sixth-seeded Radek Stepanek 4-6, 6-3, 6-3.
