Chalmers was ejected from the Heat's 110-104 victory over the Dallas Mavericks on Friday night after being called for a flagrant-2 call.
"It is disappointing about the suspension and we disagree with the suspension," Spoelstra said before Saturday night's game against the Charlotte Bobcats.
"Mario doesn't have a reputation as that type of player. ... We don't have to agree with it. What we can do is agree to disagree."
Chalmers was ejected from the game with 5:01 remaining in the fourth quarter after referees ruled he intentionally swung an elbow at Dirk Nowitzki's head. Chalmers appeared to be trying to fight through a screen set by the Mavs' Samuel Dalembert.
Spoelstra was just as concerned about the ramifications of any future flagrant foul on Chalmers.
"Mario is going to have to be very smart about it from here on out," Spoelstra said.
Chalmers has four suspension points by the NBA standards. That means he could face further suspensions with two more regular flagrant fouls or one more flagrant-2 call.
"The penalty seems very severe," Spoelstra said.
Norris Cole will start for the Heat against the Bobcats.
Chalmers posted on Twitter Saturday: "Never in my career been a dirty player. It's clear that my arm was being held and that's (what) caused me to hit Dirk. Enough is enough man."
He also added: "Can't wait until Tuesday night. It's startin to get personal now."
The Heat play at home Tuesday night against the Atlanta Hawks.Suggest a correction