The students were penalized for showing up late for class. We had to punish the dog for soiling the floor again.
source: WordNet 3.0
To impose a penalty upon; to afflict with pain, loss, or suffering for a crime or fault, either with or without a view to the offender's amendment; to cause to suffer in retribution; to chasten; as, to punish traitors with death; a father punishes his child for willful disobedience.
source: Webster 1913
To deal with roughly or harshly; -- chiefly used with regard to a contest; as, our troops punished the enemy.