The first set was a very tight affair between the two competitors with each game going by the way of serve until Berdych snatched the breakthrough.
The Czech professional looked on course to take the first set, but the British number one managed to hold his serve to force a tie-break in the opening stages, which the Scotsman clinched 7-4.
Despite a steady comeback, Murray began to struggle at the beginning of the second set, losing serve to his 26-year-old opponent, who took a 3-1 advantage early on and went on to claim the set 6-2 to level the affair.
Murray started the third in a similar fashion to the second and broke his racket after being broken in game three as Berdych took a 2-1 lead.
At 1-3 down Murray managed to hold serve after multiple deuces to keep up the pressure on the Berdych serve.
However, the Czech maintained his nerve and didn't give the Scot a look-in returning before breaking in the final game to seal a 6-3 triumph in the final set.
Berdych will play the winner of this afternoon's quarter-final between world number one Novak Djokovic and Dutchman Robin Haase.