He found the culprit, a 12-year-old schoolboy, and held him by the hair while he "pulled" his ears, the Portuguese newspaper Correio da Manha reported.
Mr Mourinho, 44, was then summoned before the headmistress and made to formally apologise to his tearful victim and his family.
The Daily Mail says shocked witnesses said the drama unfolded when the former Chelsea boss went to pick up his daughter Matilde from her £6,500-a-year bilingual school in Setubal, near Lisbon, yesterday afternoon.
One told how he watched Mr Mourinho grab Pedro Antonio and hand out his unorthodox dressing-down, and said he was left "speechless".
Isabel Simao, the headmistress of St Peter's School, said it had followed a row between the boy and Matilde Mourinho.
She said: "From what I can gather it was just a typical children's row with children's words. She claimed her dad was the best but the boy said he wasn't. It was as simple as that."
But Mrs Simao was forced to step in after seeing Mr Mourinho's furious reaction.
"I saw Mr Mourinho grabbing the child's arm,' she said. "There was no physical assault in the literal sense of the term. Pedro cried a bit at first and seemed frightened but we calmed him down.
"I asked him several times if Mr Mourinho had punched or kicked him and he denied it. But I knew that Mr Mourinho had also grabbed his hair, as the child has long hair.
"He was upset about what happened, he is after all a 12-year-old boy, but he accepted the apology."
Mrs Simao said she called Mr Mourinho and the boy's family to a meeting before the school board and said the world famous football manager presented a formal apology to the boy, his parents and the school.
Mr Mourinho's agent yesterday refused to comment on the school row.
Pedro Farrim's father Antonio said: "It is all perfectly resolved. I have nothing more to declare. For me, the matter wasn't even that important. I repeat - the matter between me and Mr Jos?ourinho is resolved."