An epic game later and struggling with a leg problem, the world No 2 will have another go at Nadal in a repeat of last week's Madrid Masters.
Djokovic masters Murray in Rome semi-final
The world No 2 took his run to 36 straight wins this year and will face world No 1 Rafael Nadal, who beat Richard Gasquet 7-5, 6-1 earlier, in Sunday's final in what will be a repeat of last week's Madrid Masters title match which Djokovic won.
But it was Djokovic, struggling with a leg problem, who demonstrated just why he has proved so hard to beat with a never-say-die attitude even when Murray was just two points from victory serving at 5-4 in the decider.
"I played my best tennis against the best player in the world at the moment," said Murray, who turns 24 on Sunday.
"It's always very physical against Novak because he moves well. I had chances to win and probably should have done."
Just as he had done in the quarter-final against Florian Mayer, Murray started very slowly and the only game he won was when he broke Djokovic in a marathon third game.
However a change of shirt, from white to blue, brought with it a change of fortunes.
In the first set Djokovic had been finding the corners and running Murray ragged around the back court before dropping little slices just over the net and out of his reach.
But in the second Murray found a way to stay in points for longer, to make Djokovic play more shots and errors started to creep into the Serbian's game.
The sixth game was the crucial one where both players showed signs of nerves but it was Djokovic who cracked, hitting a forehand long on break point.
In the decider Djokovic drew first blood, breaking in the fourth game but that proved only the prelude to five breaks in six games that saw Murray turn the match on its head and lead 5-4 with his serve to come.
Three times Murray was two points from victory but he couldn't take the extra step and a double fault made it 5-5 and a sixth break in seven.
Finally both held serve and it went to a tie-break where a Murray error handed Djokovic a mini-break and then when the Serbian passed the Scot at the net, he took a 5-1 lead.
There was no way back for Murray and Djokovic sealed victory when the Scot failed to return a drop shot.
Having lost three times to Djokovic in Masters finals this year, including last week on the clay in Madrid, Nadal has insisted he won't be the favourite on Sunday.
"There will probably be less pressure on me than before because I'll lose the favourite status and be able to play without 100 percent pressure," he said.
"I'll try my best and fight. If someone is better than you then you try to find solutions to find that level."