World number two Djokovic gained a measure of revenge for his defeat to Murray in last year's Wimbledon final with a clinical 7-5 6-3 victory in their quarter-final encounter in Miami.
The 20th meeting between these two men was the first since the Scot triumphed in straight sets at SW19 and was tainted by controversy in the 12th game of the first set.
Murray was beaten in straight-sets by Djokovic
With sixth seed Murray serving, Djokovic advanced and appeared to play the ball before it passed over the net - which is against the rules.
The point stood and Murray seemed unable to put it to the back of his mind, making three unforced errors as Djokovic wrapped up the first set.
Although Murray made a confident start to the second set and broke Djokovic for a 3-2 lead, the Serbian hit back to win the last four games to move into the semi-final.
Murray admitted he failed to take his chances but took comfort in some aspects of his performance.
"I had many opportunities like 30-all games and 0-30s on his serve, and I didn't serve so well when I went ahead in the second set," Murray said on the ATP Tour website.
"I would have liked to have done that better, but I was hitting the ball better from the back of the court.
"I was playing aggressive. I was taking the ball early. I was trying to come forward a bit. My game is not far from where I want it to be."
As for the incident that left a cloud over the encounter, Murray told reporters: "It maybe had a slight bearing on that game."