The penalty, which had left Dinamo bottom of the competition's Group A with no points, has been replaced with a fine of 75,000 euros and a suspended three-year ban from all UEFA competitions.
But Dinamo, who appealed the initial verdict, will still have to complete a two-game stadium ban and play their home match against Romanian side Timisoara behind closed doors on December 17.
They entertained Ajax Amsterdam in an empty stadium on November 5.
Dinamo welcomed UEFA's decision and said it was "a last warning" to their fans, who have a history of causing crowd trouble at away games in Europe.
"They need to change their behaviour completely before, during and after every game so that Dinamo can steer clear of the suspended sentence hanging over the club," it said on its website.
But even with the three points they collected in their 3-0 win at Timisoara, Dinamo have only a slim chance of progressing to the last 32 of the competition.
Ajax and Anderlecht top the group with eight points from four matches each, followed by Dinamo on three and Timisoara on two points.
Dinamo are away to Anderlecht in their next game on December 2 before their home game against Timisoara.
