The pair stunned the tennis world when they announced that they would be joining forces last November but the partnership has come to a halt shortly before the French Open gets underway later this month.
Djokovic said in a statement: "Thank you, coach Andy, for all the hard work, fun and support over the last six months on and off the court, really enjoyed deepening our friendship together."
The pair's collaboration got off to a strong start as Djokovic reached the semi-finals of the Australian Open in January, although the Serb had to retire from his match against Alexander Zverev due to injury.
The two former rivals had been planning to work together up until Wimbledon, but the 24-time major winner's form has declined alarmingly in recent months as he suffered shock early exits on the clay in both Monte Carlo and Madrid.
Djokovic confessed at the Madrid Open that he was facing a "new reality" after so many years as the dominant figure in men's tennis.
The former world number one said: "Kind of a new reality for me, I have to say. Trying to win a match or two, not really thinking about getting far in the tournament. It’s a completely different feeling from what I had in 20-plus years of professional tennis, so it’s kind of a challenge for me mentally to really face these sensations on the court, going out early now regularly in the tournaments."
Djokovic has taken a wildcard into the Geneva Open as he desperately looks to find form ahead of Roland Garros, where he will once again attempt to land a 25th Grand Slam crown.
In a statement of his own, Murray said: "Thanks to Novak for the unbelievable opportunity to work together and thanks to his team for all their hard work over the past six months. I wish Novak all the best for the rest of the season."