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," Williams added.
Clijsters will face Danish teenager Caroline Wozniacki, who defeated unseeded Belgian Yanina Wickmayer 6-3 6-3 in the other semi-final, on Sunday's final, Sep 13.