The former world number one believes that this "shock therapy" will help him return to the top of the game after a wretched run of results.
"I am a hunter and my biggest goal is to find the winning spark on the court again," Djokovic, 29, said in a lengthy statement on his website.
The Serb, who was knocked off top spot last November by Andy Murray, joined his rival at the exit of the Monte Carlo Masters after losing to Belgian David Goffin 6-2, 3-6, 7-5 last month.
In January, Djokovic's Australian Open title defence ended in a shock second-round exit.
The statement said Djokovic felt the need for a change and had "mutually agreed" with Vajda, fitness coach Gebhard Phil Gritsch and physiotherapist Miljan Amanovic to end their partnership.
The move follows a split late last year with coach Boris Becker after three years working together.
The 12-time Grand Slam champion said he was thinking of appointing a new head coach but did not want to rush the decision.
"I want to find a way to come back to the top stronger and more resilient," he said.
"I have so much faith in this process and that's why I will take time to find the right person who I can connect with professionally."
For now he said he would be on tour alone with the support of his family and management, with the French Open just over two weeks away.
Vajda, who has been a major influence, said he felt like he had spent a "whole lifetime" with Djokovic.
"Novak can do so much more and I am sure he will," the departing head coach said.
"I am convinced that he will remain at the top of tennis for many years and that he will bring a lot of joy to all the tennis fans around the world with his victories."