European football's governing body had been awaiting their official delegate's report before deciding what action to take over the supporter unrest which marred Wednesday night's 1-1 Group G draw in Bucharest.
Television pictures showed a number of Rangers fans clashing with Romanian police in the stands, while one supporter was seen to rip out a seat.
Police used CS gas spray during what Rangers Supporters Assembly chief Andy Kerr last night described as a "minor incident".
Responding to the charge, chief executive Martin Bain 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 to the unfolding of events within the stadium.
"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."
Reiterating his belief that over-zealous policing was partly to blame for the trouble, Bain added: "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."
Speaking today before charges were brought, UEFA's director of communications Rob Faulkner admitted the reason for the clashes required further investigation.
"As far as we can establish at the moment, it seems there were a number of Rangers supporters who came late into the stadium and we need to find out why," Faulkner told Sky Sports News.
"Then there was an issue about where they were going to sit because, apparently, there were banners already placed there which resulted in the request to remove some banners, which seems to have ended in a clash between stewards and some supporters."
Bain had last night condemned the "unacceptable" behaviour of some fans.
But he chief claimed a promise that four turnstiles would be open for visiting supporters was not kept.
When questioned over Bain's concerns over turnstile access, Faulkner said: "If that's the case, definitely [we will look at it]. If that is the case, it will be taken into account."