The Japan international faces a lengthy spell on the sidelines due to injury, while Walter Gargano will be out of action for a while, too
The left-back started the match from the bench, but came on to replace Esteban Cambiasso halfway through the second half.
His subsitute cameo lasted only eight minutes, though, as he was was forced off due to a knee injury shortly after coming off the bench and Inter have now revealed Nagatomo has a broken meniscus.
"Tests have revealed that Yuto Nagatomo broke his external left meniscus yesterday against Cagliari," a statement on the club's official website reads.
Meanwhile, Walter Gargano will be out of action for a while as well due to a thigh injury he picked up versus Cagliari.
"Walter Gargano - who came off after 53 minutes - suffered a thigh strain," Inter stated.
Inter are being plagued by injury at the moment, with Antonio Cassano, Rodrigo Palacio and Diego Milito all unavailable due to physical problems as well.