Sixth seed Berdych came from a set down to win the match 6-7 6-2 6-3 and set up a semi-final clash with world number one Novak Djokovic.
"He played better," Murray said. "I mean, I hung in, in the first set. He had some chances on my serve. Then in the tiebreak I got a few lucky bounces. He missed a couple of shots that he hadn't been missing.
"At the start of the second set it was where he obviously started playing better and my level dropped clearly, as the result suggests."
Murray will now travel to Spain to prepare for next week's Barcelona Open.