Marcus Thuram was forced off at half-time in the Champions League Round of 16 against Atletico Madrid with an adductor issue, so Inter brought on Marko Arnautovic.
The France international was trying to finish off a promising attacking move just before the break, resulting in a Jan Oblak save, but pulled up straight afterwards and needed treatment.
He held on until half-time, but was shaking his head as he walked off and it was immediately apparent he would not be able to continue.
According to Sky Sport Italia, the initial diagnosis is a twinge in the adductor of the right thigh and that will require more assessment over the next few days.
It is a blow for Inter, as Thuram has been enjoying a sensational debut season for the club since arriving as a free agent over the summer.
The 26-year-old contributed 12 goals and 11 assists in 33 competitive appearances for the Nerazzurri.
His father, former France, Juventus and Parma defender Lilian, was in the stands at San Siro to cheer on his son.