Zambrano cleaned out his locker and left the team after giving up five homers and being ejected from Friday night's 10-4 loss to the Braves. He did not return to the team Saturday.
"This was the most stringent penalty we could enforce without a release," Hendry said.
Cubs pitcher Ryan Dempster had similarly strong words.
"He's made his bed. Let him sleep in it," Dempster said.
"It's not like it's something new."
Hendry said Major League Baseball and the players' association would discuss Zambrano's statements about his baseball future.
Cubs manager Mike Quade said Friday night that Zambrano told team personnel he might retire.
"There's not much worse than running out on your teammates in the middle of a ballgame," Hendry said on a conference call.
Zambrano was ejected by plate umpire Tim Timmons in the fifth inning after throwing two inside pitches to Jones, the second going all the way to the backstop. The brush-back pitches followed homers by Freddie Freeman and Dan Uggla.
"It was uncalled for, the pitch to Chipper Jones," Hendry said.
"I feel that anything at all to detract from Bobby Cox's night other than usual competition is totally intolerable."
Asked if he knew where Zambrano was on Saturday, Hendry said: "I have no idea."
Jones said Hendry's comments were "a class move. I appreciated it."
Added Jones: "I like Carlos. I've always liked Carlos. He's an intense competitor. Unfortunately, sometimes that hurts him."
Cubs third baseman Aramis Ramirez said Zambrano would be welcomed back by his teammates, but only if he made changes.
"If he changes his attitude, he's more than welcome," Ramirez said.
"He's got to think a little bit more. He's one man. It's not just one time. A lot of people have tried to help him. He won't let them."
Zambrano was placed on the restricted list for six weeks and sent to anger management last season after a verbal altercation with then-teammate Derrek Lee.
In 2009, he was suspended following a tirade against an umpire in which he threw a baseball into the outfield and slammed his glove against the dugout fence.
Outfielder Marlon Byrd said he talked with Zambrano.
'He said that he's doing better today," Byrd said. "That's it."
Asked about Zambrano being placed on the disqualified list, Byrd said: "That's business. They have to do what they have to do."
In 2007, Zambrano signed a deal adding $91.5 million over five seasons through 2012. He was to earn $17.85 million this season and $18 million in 2012.
He is 9-7 with a 4.82 ERA.
Zambrano's name was mentioned in trade rumors before the July 31 deadline. He said on July 28 he wanted to remain with the Cubs.
"I do want to stay here but at the same point I want this team to make some changes," Zambrano said. "If we want to win here, we need to make some changes. If I have to go, I have to go but I still have the Cubs in my heart."
A message was left Saturday seeking comment from Barry Praver, Zambrano's agent. Hendry said Praver indicated Zambrano is not retiring.
The Cubs did not immediately announce a corresponding roster move for Zambrano. The team will need a starting pitcher for Zambrano's next scheduled turn in the rotation Wednesday at Houston.
AP freelance writer Amy Jinkner-Lloyd in Atlanta contributed to this report.