Just weeks after returning to the tour from a two-year break to start a family, Clijsters beat the defending champion 6-4 7-5 after a day-long rain delay at Flushing Meadows.
At 5-6, 15-30 down in the second set, Williams whacked her second serve but the lineswoman called her on a foot-fault for a double fault that put her at match point.
The American's subsequent tirade against the lineswoman resulted in a point penalty—and the end of the match.
"All year I've never been foot faulted, and then suddenly in this tournament they keep calling foot faults," said Williams. "I said something that I guess they gave me a point penalty for. Unfortunately it was on match point."
In Sunday's final, Clijsters will face Danish teen-ager Caroline Wozniacki, who defeated unseeded and error-prone Belgian Yanina Wickmayer 6-3 6-3 in the other semi-final.
Earlier Saturday, third seed Rafael Nadal needed just 34 minutes to complete a rain-delayed 7-6 7-6 6-0 victory over Chile's Fernando Gonzalez and gain a spot in the semi-finals.
Nadal will face sixth seed Argentine Juan Martin del Potro, one of the hottest players on the tour this summer.
"He's a very complete player," Nadal said of Del Potro. "In the past, he didn't serve like he is doing right now. He has an unbelievable serve right now. From the baseline, he is very solid. He doesn't make mistakes."
In Sunday's other other men's semi-final, five-times champion Roger Federer faces fourth-seeded Serb Novak Djokovic, both players well-rested after having three days off.
Well-Earned Win
The contentious ending of Clijsters' match marred her well-earned victory.
"It's unfortunate that a match that I was playing so well at had to end that way," said Clijsters, the 2005 Open champion and former world number one.
"Obviously, I still to this point am a little confused about what happened out there, just because I was so focused. I was trying to win that last point. Things ended a little bit different than I expected."
Clijsters became the first mother to reach a grand slam final since Evonne Goolagong at Wimbledon in 1980.
Exactly what Williams said to the lineswoman was not revealed publicly, though at one point during the dispute at the umpire's chair she was heard telling the lineswoman: "I never said I would kill you, are you serious?"
Williams, the 2009 Wimbledon and Australian Open champion, said she did not believe the lineswoman "understood it was a point penalty, which meant that I lost that point, which meant that I lost the match.
"Obviously I wanted to fight," she said. "I always fight when I'm down and keep going. I planned on hitting a couple of aces, but I guess it didn't work out."
In a match delayed more than seven hours because of wet conditions, unseeded Wickmayer made 40 unforced errors, mainly from her booming forehand, against just 14 for Wozniacki.
"I'm in the U.S. Open final, I cannot describe it with words," said Wozniacki. "I'm so excited. It's a dream come true to play the finals of a grand slam, and now I'm here.
"I have absolutely nothing to lose."
Nadal resumed his quarter-final leading 7-6 6-6 with Gonzalez serving at 2-3. The Spaniard won the first four points to clinch the second set, and Gonzalez unraveled.
The Chilean committed more unforced errors in the third set (21) than Nadal had in the entire match (13).
"I get afraid maybe in the tiebreaker," said Gonzalez. "I went for it. I did a good play, miss one. The next play I miss another one, then I miss another one.
"What else can I do? I try my best."
