Opposing supporters clashed in the stand during the 2-2 first-leg draw on August 2 and United confirmed that UEFA's control and disciplinary body had also punished them for a pitch invasion in the third qualifying round match.
United confirmed they would not appeal and chairman Stephen Thompson said: "It is extremely disappointing that the actions of a few individuals have imposed this financial penalty on the club. We are working alongside Tayside Police to identify the individuals involved in the crowd disturbance and the person who encroached on the pitch has already been notified of a lifetime ban."
Fans clashed in the Jim McLean Fair Play Stand when supporters from the visiting section climbed up into the upper tier, which housed United fans.
Tayside Police said three fans had been arrested and seven ejected from the ground on the night.