The 12th-seeded Czech used his big serve and forehand to beat Federer in four sets, 6-4, 3-6, 6-1, 6-4, on Centre Court for the biggest victory of his career.
It's the first time since 2002 that Federer has failed to reach the final. Since losing in the first round eight years ago, Federer had won the title six times and finished runner-up once, bolstering his reputation as the greatest player of all-time.
Winner of a record 16 Grand Slam titles, Federer was clearly outplayed by a man who has always possessed enormous talent but often failed to live up to expectations.
The 6-foot-5 Berdych was on the offensive for most of the match, hitting 51 winners, compared to 44 for Federer.
Berdych broke Federer four times, with the decisive break coming in the seventh game of the fourth set. Berdych, hitting first serves consistently in the 130s mph, served 12 aces and was broken just once.
"It's really tough to show this crowd how I'm just feeling right now, it's amazing to play on this stadium to play such a great player as Roger is, and come here and be here as a winner is just really amazing," Berdych said.
Berdych ripped a clean forehand winner on his second match point.
"If I can just go through my career, it was so far the toughest game to serve and close out the match," he said.
Federer came in with an 8-2 career record against Berdych, having lost the first match at the 2004 Athens Olympics and the last in Miami this year.
Federer was playing in his 25th consecutive Grand Slam quarterfinal. He had won 23 straight, but now has lost two in a row. Federer fell to Robin Soderling at the French Open earlier this month.
Federer had won 76 of 77 grass-court matches dating to 2002 coming into this month, but has now lost two of the past six, including to Lleyton Hewitt in Halle, Germany, the week before Wimbledon.
With the loss, Federer will drop to No. 3 in the ATP rankings next week for the first time since Nov. 10, 2003.
Berdych will next face Novak Djokovic, who swept past Yen-hsun Lu in straight sets to reach the semifinals or the second time.
The third-seeded Djokovic never faced a face break point as he beat the 82nd-ranked Taiwanese player 6-3, 6-2, 6-2 in less than two hours on Court 1.
Lu stunned three-time finalist Andy Roddick in the quarterfinals, but couldn't replicate that performance against the 2008 Australian Open champion.
Djokovic lost just 12 points in 13 service games. He won 26 of his first 28 service points, including 15 in a row. The Serb had 29 winners and 17 unforced errors, and converted five of 15 break points.
"Nothing is easy these days, especially at this stage of the tournament," Djokovic said. "But the way I played, I deserved to win. I was hitting all the shots and I was really playing very solid from all parts of the court. I'm very, very happy with the performance today."
Djokovic reached the semifinals here in 2007 but had to retire against Rafael Nadal with a foot injury while trailing in the third set.
"This time physically I'm fitter," Djokovic said. "Those were very strange conditions and circumstances. I had to play three very long matches in three days and couldn't hold on in the semifinal. This time everything is in order and Ill give my best."
In other matches, No. 2 Nadal played No. 6 Robin Soderling, and No. 4 Andy Murray faced Jo-Wilfried Tsonga.
The women's semifinals are Thursday, with an unusual final four featuring Serena Williams and three unheralded players.
Defending and three-time champion Williams plays 62nd-ranked Petra Kvitova of the Czech Republic, while 82nd-ranked Tsvetana Pironkova of Bulgaria will face No. 21 Vera Zvonareva of Russia
Missing is five-time champion Venus Williams, who played in eight of the past 10 women's finals but was upset in straight sets by Pironkova in the quarterfinals.
There was a surprise in the women's doubles Wednesday with the top-ranked Williams sisters losing 3-6, 6-3, 6-4 in the quarterfinals to Russians Elena Vesnina and Vera Zvonareva.
The loss ends the American pair's hopes of winning the Grand Slam this year after victories at the Australian Open and French Open. They had won four straight Grand Slam titles and were shooting for their 13th Grand Slam title and fifth here.