It's very literal.
Whatever it is he did, he did it one time too many and suffered a bad result.
Perhaps he made the teacher mad on many occasions, and this time, she sent him to the principal's office. He made her angry once too often.
Maybe you teased someone many times, but this time, you teased him and he knocked you to the ground. You teased him once too often.
[not a teacher]
Student or Learner