Polish qualifier Jerzy Janowicz will face Gilles Simon in the semi-finals of the Paris Masters after both players claimed upset wins on Friday.
French world No.18 Simon delighted his home crowd with a 6-4 6-4 victory in one hour and 51 minutes against Berdych.
However, the fifth-seeded Berdych will rue his missed opportunity to take the match into a deciding set - having led 4-1 in the second.
But Simon reeled off five games in a row, breaking twice and then saving three break points from 0-40 in what turned out to be the final game of the match.
Although Berdych fired down five of the contest's seven aces, he was only able to convert one of 10 break point opportunities.
It was Simon's fifth win in seven meetings with Berdych, who now heads to London for next week's ATP World Tour finals at the O2 Arena.
Simon, who has never won a Masters Series event, has taken advantage of top seed Roger Federer's withdrawal at the top end of the draw.
Janowicz, meanwhile, continued his fairytale run at the tournament when eighth seed Janko Tipsarevic retired during the third set of their quarter-final clash.
Janowicz, who ended the challenge of Andy Murray on Thursday, lost the first set but had recovered to lead 3-6 6-1 4-1 by the time his Serbian opponent pulled out.