UEFA said in a statement on Monday that both federations were facing charges for "setting off fireworks" and the "throwing of objects" at Lyon's Parc OL.
Albania faced additional charges for "field invasion", the statement added.
Albania won the game 1-0 to clinch third place in the group and maintain hopes of qualifying for the knockout stages while Romania were eliminated.
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(Reporting by Julien Pretot; Editing by Neil Robinson)
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