Heavy traffic caused the hosts to arrive late at Old Trafford for the clash against Los Che, who were also sanctioned for setting off fireworks.
Manchester United have been fined €15,000 for the late arrival and subsequent behind-schedule kick-off of their Champions League game with Valencia, while Napoli must pay €34,000 for the setting off of fireworks against Liverpool.
United were affected by heavy traffic congestion in Manchester ahead of the match on October 2, which finished 0-0.
The club confirmed 25 minutes prior to the initial kick-off time of 20:00 BST that the match had been delayed until 20:05 BST due to the late arrival of their bus.
UEFA has fined them €5,000 for the late arrival of the team, and €10,000 for a delayed start to the match, while Valencia will pay €1,000 for the setting off of fireworks.
Napoli's fine is significantly larger, however, after UEFA charged them for the same offence as Valencia at Stadio San Paolo during the 1-0 win over Liverpool on October 3.
The Serie A club were also found guilty of blocking stairways in the stadium, as were CSKA Moscow during their 1-0 defeat of Real Madrid, copping a €12,000 fine.
And CSKA's trip to Viktoria Plzen in September is also the subject of a financial penalty for the Czech side, who must pay €10,000 for the throwing of objects during the game.