The game between Luxembourg’s F91 Dudelange and Azerbaijan’s FK Qarabag was halted in the first half by the drone, which appeared to be carrying the flag of the disrupted region of Nagorno-Karabakh.
Azerbaijan and Armenia are in a territorial dispute over the region.
The drone incensed Qarabag players, who tried to hit it with the ball as it flew over the centre circle.
Play later resumed, with Qarabag winning 4-1.
UEFA said the decision to halt the match was taken “for safety and security reasons”.
The European governing body said in a statement: “UEFA will await the official reports from the match officials to determine whether disciplinary proceedings will be opened.”
F91 Dudelange also tweeted: “We apologise to guests from Azerbaijan. We have nothing to do with this provocation. We’ll figure out!”
A fan carrying the Nagorno-Karabakh flag also ran onto the pitch during Qarabag’s away game at Arsenal in last season’s Europa League.
Nagorno-Karabakh is a region of Azerbaijan which has been under the control of ethnic Armenian forces backed by Armenia since a war there ended in 1994.