Major League Baseball also handed down a three-game suspension and a fine for right-handed pitcher Aneury Rodriguez, who is appealing the suspension and was available to pitch. There is no appeals process for managers, meaning Mills had to serve his suspension immediately.
"I disagree with it whole-heartedly," Mills said.
Astros bench coach Al Pedrique managed Tuesday's game.
Joe Garagiola Jr., baseball's senior vice president of standards and on-field operations, called Astros general manager Ed Wade at about 2 p.m. CT on Tuesday to inform him of the suspensions. Mills later pleaded his case in a conference call with Joe Torre, who was recently appointed as baseball's executive vice president for baseball operations. The decision was upheld.
"Joe listened and was very respectful throughout his conversation and just felt that past practice dictated this was the right way to handle it," Wade said. "In Aneury's case, there is a formal appeals process for a player and that will go through the Players' Association, and hopefully once that hearing takes place the suspension will go away. It would be nice to be able to think at the very least it would be reduced."
The suspensions and fines were the result of a pair of hit batters in Sunday's game against the Marlins, an incident that appeared to stem from Bill Hall's hard slide into Marlins shortstop Hanley Ramirez on Friday. Ramirez was injured and missed the final two games of the series, but said the slide was clean.
Marlins reliever Edward Mujica hit Hall with a pitch in the seventh inning of Sunday's series finale and was ejected, and both benches were warned. Rodriguez, a Rule 5 pick, struck Marlins first baseman Gaby Sanchez with a pitch in the ninth inning and was ejected along with Mills.
The Astros contend Mujica, who was fined and not suspended, intentionally hit Hall in retaliation for his slide, and that Rodriguez simply had a pitch get away from him.
"We're sorry Hanley was hurt for two days," Mills said. "He didn't go in there trying to hurt him. There was no intent to hurt, and we felt they threw at our guy and Bill Hall went to first base and there was no intent on our side. Six pitches [into Sanchez's at-bat] and he happens to get hit, and you have a lot of respect for Gaby Sanchez.
"He dropped his bat and ran to first base. Nothing was incited, nobody wanted to fight anyone, nobody was screaming or yelling at anyone. That's kind of the crux of what I had to say [to Torre]. I was mostly defending Aneury. I felt that was just not fair."
Rodriguez declined comment because his case is under appeal, but said Sunday he was simply trying to pitch inside. Hall is surprised so much has come about as a result of his slide into Ramirez at second base.
"I've heard there's been some reports on TV and the Internet -- 'Was it a dirty slide? Was it a clean slide?'" he said. "[The opinions] are kind of half and half. Like I said, sometimes it's out of the other players' control. No matter what he thinks, 24 other guys might have thought differently and thought I could have done something different to try to avoid him.
"It's not going to stop me from playing the game hard; it's not going to stop any of us from playing the game hard. I'm going to continue to play hard and battle, and if we keep battling, things are going to come into place."
In the rules and regulations bulletins each team receives prior to the season, Wade said there is no stipulation that a manager will be automatically suspended if a pitcher throws at a hitter after the umpire issues warnings. Major League Baseball does have the discretion to issue further penalties, which it did in this case.
"There's a line that says the Commissioner's Office reserves the right to hand out further discipline if they feel it warranted, but we didn't feel it was warranted," Wade said. "We had our day in court. Millsie had a chance to talk to Joe Torre about it, and Aneury will have a chance through the appeals process through the Players' Association to have his day in court."
Wade believes Mills and Rodriguez were suspended because of precedent.
"That's the way these things have been happening, and we don't necessarily agree with the decision to suspend both Mills and the player," he said.
Brian McTaggart is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.