Murray took one hour and 51 minutes to dispose of the former Wimbledon finalist from the Czech Republic, winning 6-3, 7-5.
Murray has struggled with a knee injury throughout the tournament and asked about his ailment, he said: “I had a problem with it since Brisbane and it’s come and gone.
“It was a bit sore right before the tournament. I didn’t feel it at all in the first couple of matches, and then right at the beginning of the second set I felt it.
“It’s not something that stops me sort of running around. I want to try and get rid of it, because there are a lot of the big events coming up.”
Murray will face Djokovic for the first time since their epic semi-final in Melbourne in January which the Serb won in five gruelling sets.