Williams, the world number one and defending champion, won a disappointing semi-final in exactly 80 minutes, making 37 unforced errors herself.
Clijsters, the third seed, did the hard work for her opponent, the Belgian squandering chance after chance with a succession of misjudged shots and mustering only six winners in the match.
The defeat was Clijsters's seventh in eight meetings with Williams, the holder of all four grand slams. He moves through to the final of the $2.96 million tournament on Saturday against Jennifer Capriati or Chanda Rubin.
"My game was just passing grade today," Williams said. "I wasn't too happy with the way I played. My trainer says I played okay, but I'm always really hard on myself and I don't think I was on par.
"Kim was still playing hard and tough, and it was a tough match. I upped my game a little bit."
The final will be Williams's third since her Miami debut in 1988, when she lost to former world number one Martina Hingis in the quarters.
The Stadium Court grandstands were less than a quarter full when Clijsters began the match by dropping her serve in the first game.
She broke straight back when Williams struck a backhand into the net but mistakes from both players provided the story of the match.
Clijsters wasted two break points at 2-1 in the first set, sending her forehand wide, and another at 2-3 when the ball hit the net and bounced back.
She also missed several game points on her own serve, opening the door for her opponent.
Williams fared little better with her own accuracy, finding the net regularly with forehands and backhands that would usually sail for winners.
BACKHAND WINNER
Her best game was the 10th as she struck only her second ace to give herself three set points before clinching the set with a fierce backhand winner.
Clijsters was in trouble from the start of the second set, dropping serve in the first game and falling a double break behind when Williams's forehand down the line followed a double fault.
Clijsters saved four match points on her own serve at 1-5, three through Williams's errors, but the reprieve was only temporary as Williams raced to 40-0 in her final service game and closed out the match with an ace.
It was another frustrating afternoon for Clijsters, who allowed Williams to save two match points and recover a 5-1 final-set deficit in the Australian Open semi-final in January.
The Belgian's only previous victory over the undisputed world number one came at the 2002 WTA season-ending Championships in Los Angeles.
On Thursday's showing, it will be a long time before she manages a repeat.
