Roma progressed with a 2-1 win in Rotterdam, handing them a 3-2 aggregate success following a fiery encounter during which the hosts saw Mitchell te Vrede and Erwin Mulder shown straight red cards.
The game was marred by the apparent racial abuse of Gervinho by Feyenoord fans, with an inflatable banana thrown at the Giallorossi forward from the stands.
The Dutch club face charges for racist behaviour, which caused delays to the encounter, together with the "setting off and throwing of fireworks and/or objects" and "insufficient organisation".
Roma forward Adem Ljajic, meanwhile, will also face action for provoking spectators, while the Italian club have been charged for breaching regulations relating to a "late kick-off".
The case against Feyenoord will be heard by Uefa's control, ethics and disciplinary body on March 19, while Roma and Ljajic are set to discover his fate on March 4.