Romania face action after fans set off fireworks and threw objects, with Albania accused of the same offences in addition to allowing a pitch invasion.
The charges mean that eight of the 24 teams competing in the tournament are the subject of disciplinary probes.
Albania won the Group A match 1-0 to maintain slim hopes of progressing while eliminating Romania.
Uefa has opened proceedings against Albania and Romania after incidents in Sunday's Euro 2016 match in Lyon.