The cheerleaders put the condoms in the bags a week ago, the Wharton Independent School District said.
The district said the incident was a violation of the student code of conduct. The girls received a one-day school suspension and were banned from Friday's game.
Some parents said the punishment was too harsh.
"If they did that, it was just a joke," Teresa Holmes, a parent, said. "They need to go on with that and let children be children."
The district said in a statement the punishments are based on state law and are intended to teach students proper behavior.