The two former rivals worked together since November last year and joined forces at four tournaments in 2025, with the collaboration bringing mixed results.
In his first tournament with Murray in his box, Djokovic reached the Australian Open semi-finals having beaten Carlos Alcaraz in the last eight, before a hamstring injury forced him to retire against Alexander Zverev.
Djokovic also made a run to the final at the Miami Open with five dominant straight-set wins before he lost to Jakub Mensik.
The 37-year-old lost his opening match at the other two events: in Indian Wells and Madrid.
It had been expected that Djokovic and Murray would continue their partnership at the French Open and Wimbledon, but both confirmed they had parted ways on Tuesday.
In a post on social media, Djokovic said: "Thank you, coach Andy, for all the hard work, fun and support over last six months on and off the court. I really enjoyed deepening our friendship together."
Murray added: "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."