Nagatomoâ€™s Nerazzurri teammate Esteban Cambiasso cancelled out Gonzalo Higuainâ€™s ninth minute opener after the half-hour mark before the Partenopei opened up a two-goal lead through Dries Mertens and Blerim Dzemaili by the 41st minute.
Japan international Nagatomo found himself unmarked at the back post in the 52nd minute to slot home Fredy Guarinâ€™s low effort to give the visitors some semblance of hope at the Stadio San Paolo.
However, Ricky Alvarez was sent off for a second bookable offence in the 71st minute which further disadvantaged Inter who then fell further behind when Jose Callejon netted late.
The goal was Nagatomoâ€™s fourth Serie A tally of the campaign but did nothing to improve Interâ€™s standing on the table as they dropped to fifth behind Fiorentina.
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