Zambrano was ejected from a game against the Atlanta Braves on Aug. 12 after he gave up five runs in an inning and then brushed back Chipper Jones twice. Zambrano left before the game was over and told a clubhouse attendant that he was retiring.
The Cubs placed Zambrano on the disqualified list, which means he couldn't play or be paid, on Aug. 13. In the negotiated deal with Zambrano and his agent, the pitcher agreed not to return for the rest of the season, but he started getting paid again on Sept. 11 when he came off the disqualified list.
As part of the deal, Zambrano was not put back on the 40-man roster until Thursday, the day after the regular season ended. The players association is grieving the 30-day disqualification and the money lost by Zambrano during that period of time.
The Cubs owe Zambrano $17.885 million in 2012 and hope to be able to trade him and a portion of that money owed during the offseason.
Also, Cubs pitcher Kerry Wood is scheduled to undergo arthroscopic surgery on his left knee on Friday followed by six weeks of rehab. Wood suffered the injury while squatting in the bullpen on Sept. 17 and missed the season's final 10 days. A free agent, Wood said he would like to return to the Cubs but will retire if the club doesn't want him back.
ESPNChicago.com's Bruce Levine contributed to this report.