The European governing body UEFA said Dinamo, who beat the Romanians 3-0, would also have to play their next two home games in the competition behind closed doors following the latest bout of trouble involving Croatia supporters.
"The decision follows serious crowd disturbances at the UEFA Europa League match between Timisoara and Dynamo Zagreb on 1 October," UEFA said in a statement.
"The two home matches to be played behind closed doors are against Ajax on 5 November, and Timisoara on 17 December.
"The three-point deduction is effective immediately and is taken from the total number of points achieved by Dinamo Zagreb in Group A."
The decision leaves Dinamo bottom of Group A with no points from three games.
Dinamo Zagreb officials said the club would file an appeal.
"We're embittered by the fact that a small number of fans have inflicted such a huge damage to the image of our club. We'll certainly file an appeal and offer arguments which might help to mitigate the sanction," Dinamo's director Damir Vrbanovic told state radio.
Croatia's soccer association has been fined regularly in recent years for the violent behaviour of fans, who have chanted racist abuse and clashed with police at home and abroad.
Two weeks ago, Croatia Prime Minister Jadranka Kosor said authorities must seriously consider interrupting soccer games and live television broadcasts to stamp out violent or rude behaviour by fans.
"Soon, we will most likely propose stricter laws on suppressing violence and improper behaviour at sports events," she said.
Her comments came after a group of Croatia fans chanted ethnically motivated insulting slogans during an Under-21 international against Serbia in the northern Croatian town of Varazdin, which was broadcast live on state television.
The Varazdin city authorities apologised to the Serbian soccer delegation for the incidents.
