The Cubs will resume paying Zambrano his salary at the end of his 30-day suspension, which is set to expire on Sept. 11.
Major League Baseball, the Major League Baseball Players Association and the Cubs will process the union's grievance during the offseason.
"It was just a disappointing situation," Cubs manager Mike Quade said. "I'll let things take their course now."
The Cubs placed Zambrano on the disqualified list when he cleaned out his locker in the middle of the Aug. 12 game in Atlanta after he was ejected for throwing two inside pitches at Chipper Jones. Reports indicated he emptied his locker mid-game and told club personnel he was retiring.
Before Friday's game, Quade said he believed Zambrano could still play in the future and be productive in the Majors.
"He still has something to offer," Quade said. "His numbers [show] that."
Zambrano, 30, has one more guaranteed year, at $18 million, left on his contract.
Sam Zuba is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.