The 19-year-old Croatia international, who signed for Inter from Dinamo Zagreb in January, was forced off at the end of the first half of the Serie A clash.
Coach Walter Mazzarri told Sky Italia: "I don't know how serious his injury is. We'll run some tests on him but I don't think it's that bad."
Rodrigo Palacio and Yuto Nagatomo were on target at the Stadio Angelo Massimino while Ricky Alvarez cemented a result which maintained Inter's 100 per cent record this season.
The Nerazzurri finished a dismal ninth last season but, under the supervision of former Napoli boss Mazzarri, claimed a regulation victory over Genoa on the opening day of the new campaign and - after Sunday's win - currently sit fourth in the table.
Mazzarri is confident they can continue to remain with the clubs at the top of the league, and he added: "I'm satisfied but we must keep improving.
"We're still making mistakes in possession. We need to be more clinical at times too. We have to keep growing if we want to stay in the mix at the top."
And he praised the progress of his squad, saying: "Jonathan and Nagatomo did well, they've come on a lot.
"The whole team is on the up in general.
"They were still feeling the psychological effects of last year - you should have seen how tense they were before (Coppa Italia opponents) Cittadella.
"Now we're gaining in confidence, winning games always helps in that respect."