Clijsters exhausted the 17-year-old Czech in long rallies and kept her off balance by varying the speed of her replies.
"When you play younger players, they go out and have nothing to lose but once it gets close, that's when experience can play a role and they can get frustrated," said the U.S. Open champion.
The world number two will now face the winner of the second semi between second-seeded Swiss Patty Schnyder and the unseeded Tatiana Golovin of France.
The Belgian got off to a slow start when she was broken to go 2-4 when Vaidisova ripped a backhand winner down the line.
Clijsters broke back and then fought off a set point with a second serve ace down the tee at 4-5 and then found her stride to lead Vaidisova 6-5 when the Czech miscued a forehand.
A frustrated Vaidisova, who had trouble containing her temper all day, then hit a ball toward her stepfather and coach, Alex Kodat, who was sitting courtside.
"I don't feel my temper had an effect on how I played but emotions are part of the game and I'll always be that way," said Vaidisova, who doubled-faulted 10 times. "I just had no rhythm on my serve."
Clijsters then took the set on her fifth set point when she smoked a service winner.
Vaidisova, who beat Amelie Mauresmo and Venus Williams en route to the French Open semi-finals, then lost her way.
Clijsters won 14 straight points early in the second set and broke her opponent twice before holding to love to win the match when Vaidisova missed an easy forehand.
"My level is getting better with each match," said Clijsters, who has won the Bank of the West title three times and has won 11 straight matches at the event.
"That's what you try to aim for. I'm not at my best yet, but I want to improve and when you want to, that's when you will."
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