Germany defender Rudiger left Roma for Chelsea last summer, having previously expressed his frustration at a failure to tackle racist incidents which saw him targeted.
UEFA said the charge was “racist behaviour (monkey chants)”, adding: “This case will be dealt with by the UEFA Control, Ethics and Disciplinary Body on November 16.”
Rudiger, 24, appeared in Wednesday’s fixture as a 77th minute substitute.
Before his departure from Roma in May, for an initial £29million, he told German sports magazine SportBild : “Racism is a serious issue here.
“Incidents like the ones with (Juventus’ Medhi) Benatia and me simply happen too often in this country and that is why something must happen now. When the Italian FA is not doing anything then FIFA must act.
“It is easy to come up with the ‘No to racism’ campaign but when you don’t do anything concrete then that does not help.”
Chelsea had taken a 2-0 lead against the Italians on Wednesday before falling 3-2 behind and eventually securing a draw through Eden Hazard’s equaliser.