The team announced Friday it will resume paying the right-hander's salary after his 30-day suspension ends Sept. 11, but he won't return to the team because there would be "insufficient preparation time" for him to pitch again this season.
Zambrano's latest run-in with the team started Aug. 12 when he gave up five homers against the Braves, then was ejected for throwing at Chipper Jones. He cleaned out his locker and left the park before the game was over, telling clubhouse personnel that he was retiring.
Jim Hendry, then the Cubs' general manager, put Zambrano on the disqualified list, resulting in the suspension without pay and keeping him away from all team activities.
The players' union filed a grievance, which the Cubs said Friday has not been resolved. The team said that Major League Baseball, the union and the Cubs will process the grievance during the offseason.
"It was a disappointing situation and we'll let things take their course now," manager Mike Quade said Friday before a game against the Pittsburgh Pirates at Wrigley Field.
"That's it, let's see where the grievance situation goes. They've made decisions and that's where we're at now."
Zambrano has spent his entire 11-year career with the Cubs and is a three-time All-Star, but his years in Chicago have been filled with controversy.
In 2007, Zambrano got into an altercation with teammate Michael Barrett in the dugout, where punches were thrown.
In 2009, he was suspended six games by MLB for throwing a ball into left field, tossing his glove and destroying a Gatorade dispenser in the dugout.
In 2010, he got into a jawing session with first baseman Derrek Lee in the dugout at U.S. Cellular Field after a rough first inning against the White Sox. Zambrano was suspended for six weeks, had to attend anger management classes, and when he returned was relegated to the bullpen.
Earlier this season he blasted Carlos Marmol for his pitch selection after the closer blew a save in one of his starts and called the Cubs "a Triple-A team."
Zambrano is still owed $18 million in 2012, the final year of his five-year, $91.5 million contract.
Information from The Associated Press was used in this report.