Berdych, the Czech world number 14, only teamed up with Ivanisevic in August last year.
However, a second round exit at the French Open prompted the 31-year-old to seek a new direction.
"Goran and I will not be working together anymore," Berdych wrote on Facebook.
"I enjoyed the ride and we will remain great friends."
"Wish him all the best in the future and I am committed to go after my goals with current team," said Berdych, who bowed out of Roland Garros after a straight sets loss to Russian youngster Karen Khachanov.
Ivanisevic previously coached fellow Croat Marin Cilic, a partnership which yielded the US Open title in 2014.
Berdych, the 2010 Wimbledon finalist, hired Ivanisevic in August 2016 with a view to a first-ever Grand Slam title.
He won the Shenzhen Open under Ivanisevic's guidance in October, but soon slipped out of the top ten for the first time in more than six years.