The NL-Central worst Pirates fired Hurdle, 62, after a 69-92 finish this season, the club's worst record since going 57-105 in the 2010 campaign.
Hurdle had two years remaining on his contract. He had been MLB's third-longest-tenured manager, trailing only the retiring Bruce Bochy of the San Francisco Giants and Kansas City Royals skipper Ned Yost.
"Words cannot express how much respect and appreciation I have for Clint as a person and a leader," Huntington said in a statement. "He was the right person at the right time to take on the enormous challenge of leading our Major League team out of an extended losing streak and piloting us to three straight postseason appearances.
"We will be forever grateful for his dedication to the Pirates organization on and off the field. This was an extremely difficult decision for us. As an organization, we believe it was time for a managerial change to introduce a new voice and new leadership inside the clubhouse."
Huntington will remain in his position with the franchise, Pirates chairman Bob Nutting said in a statement.
"While we felt it was time to make a change at the managerial level, I strongly believe Neal Huntington and the leadership team that he has assembled are the right people to continue to lead our baseball operations department," Nutting said.
The Pirates hired Hurdle as manager in 2011. He led the club to winning seasons in four of his nine years, including three trips to the postseason.
Pittsburgh's last trip to the playoffs came in a 2015 National League wild-card loss to the Chicago Cubs. Hurdle finished with a 735-720-1 record over his nine seasons with the Pirates.