The case will be dealt with by the control and disciplinary body next Thursday.
"As far as we can establish it seems there were a number of Rangers supporters who came late into the stadium and we need to find out why," UEFA's director of communications Rob Faulkner told Reuters on Thursday.
"There was then an issue about where they were going to sit because, apparently, banners were already placed in their seats which resulted in the request to remove some banners which seems to have ended in a clash between stewards and some supporters."
European football's governing body charged Rangers after receiving a report from its match delegate at the Group G game in Bucharest.
Television pictures showed Rangers fans clashing with police who used CS gas to try and control the situation.
Rangers chief executive Martin Bain told the club's website they "would fight the fans' corner."
SAFETY OF FANS
He said: "We have been informed by UEFA that disciplinary proceedings have been instigated in relation to the throwing of missiles and crowd disturbances.
"As already stated I am not for a moment condoning the action of some supporters ... but as a club the preparations which were agreed and insisted upon in advance were not adhered to and this in turn we feel jeopardised the safety of our supporters."
Bain said over-zealous policing was partly to blame for the trouble, adding: "We are fully aware of the indiscriminate use of CS gas and the difficulties experienced by our fans accessing the stadium.
"All these factors will be presented fully by the club to UEFA in our submission."
