Five-time champion Federer departed Flushing Meadows before the semifinals for the first time since 2003, stunned by the sixth-seeded Berdych 7-6 (1), 6-4, 3-6, 6-3 on Wednesday night.
"I just didn't come up with the goods tonight," Federer said. "It was unfortunate."
His famous forehand was way off for much of the evening: 24 of his 40 unforced errors came off that wing. The 6-foot-5 Berdych, meanwhile, kept pounding serves and groundstrokes right where he wanted them, finishing with a total of 14 aces, 30 winners and only 21 unforced errors.
"There is no better moment than this one so far," said Berdych, who will face Olympic champion Andy Murray in the semifinals Saturday.
Murray beat Marin Cilic 3-6, 7-6 (4), 6-2, 6-0. He trailed 5-1 in the second set before breaking twice to come all the way back.
In the tiebreaker, Cilic had a 4-2 lead and a point on his serve, but Murray ran off five consecutive points to even the match. The third-seeded Brit won the last 11 games to wrap up the victory in 3 hours.
For Berdych, it was his fourth victory in his past seven meetings against 17-time Grand Slam trophy winner Federer, including in the 2010 Wimbledon quarterfinals en route to a runner-up finish to Rafael Nadal at the All England Club.
Federer hadn't competed since Saturday, and he looked rather rusty, particularly for the first two sets Wednesday. The man he was supposed to play in the fourth round Monday, Mardy Fish, withdrew because of a health scare.
In dark sneakers bearing a tiny gold trophy with a black "5'' etched on it - representing his title count at the U.S. Open - the top-seeded Federer failed in his bid to reach the semifinals in New York for the ninth consecutive year.
He won the championship every year from 2004 through 2008, but his 40-match winning streak at the hard-court major tournament ended with a loss to Juan Martin del Potro in the 2009 final. Federer then was beaten by Novak Djokovic in the semifinals in 2010 and 2011.
This year, Federer took another step backward, bothered by another big hitter.
Berdych absolutely controlled the opening-set tiebreaker, capping it with a 128 mph ace.
And then, quick as can be, he broke to begin the second set, first smacking a superb forehand winner down the line on a full sprint, then watching Federer miss two wild forehands on consecutive points.
Berdych broke again in the third and led 3-1 there before Federer began to find his form, briefly making this interesting. Berdych also hurt himself, showing signs of nerves by double-faulting twice while getting broken to 3-all.
That was part of a stretch in which Federer looked a lot more like, well, Roger Federer, taking four games in a row and 19 of 24 points to take the third set. He ended it with a perfect drop shot, and all of a sudden, the possibility of a ninth career comeback from a two-set deficit seemed possible.
Berdych, after all, had blown such a lead to Federer before, in the fourth round of the 2009 Australian Open.
Not this time, though.
At 2-2 in the fourth, Federer conjured up a terrific cross-court backhand passing winner that left Berdych skidding and stumbling as he tried to change directions while moving toward the net. Berdych dropped his racket as he fell, scraping his fingers along the blue court.
After taking several seconds to compose himself - and to press a cold water bottle against his hand - Berdych lost the next point, too, to fall behind love-30, then took the next four points to hold for a 3-2 lead.
And three games later, Berdych smacked a cross-court forehand winner to break Federer and make it 5-3.
All Berdych had left to do was hold serve once, and he did it, delivering a 124 mph ace to get to match point, and a 124 mph service winner to convert it.
"When you leave it a little bit on Roger's game, and he starts to go for it, it could be a really big problem," Berdych said. "So I was just trying to get it back, trying to get my rhythm back again, and to stay as close as possible. And finally it was the right moment, right tactics."