Oleg Gusev grabbed an early lead in just the third minute before a 34th-minute Josip Pivaric own goal ensured a comfortable night.
After suffering a 4-1 humbling in their opener against Paris St Germain a fortnight ago it meant Dynamo immediately bounced back with their first points of the campaign.
For their beaten visitors it was an eighth consecutive defeat in the group stage of the Champions League.
Dynamo took just three minutes to go ahead when Ukraine midfielder Gusev ran onto a perfectly-weighted Ognjen Vukojevic cross.
Gusev sprinted in front of his marker to meet the ball and get just enough of a touch to help it past Ivan Kelava.
Dynamo assistant coach Sergei Rebrov singled out visiting striker Jorge Sammir as the main threat in the lead-up to the game and his warning was heeded early as Damilo Silva got out to block Sammir's effort from 12 yards.
Dynamo were otherwise untroubled in the first half and after Miguel Veloso saw his free-kick tipped over by Kelava the hosts grabbed a second in slightly fortunate circumstances.
Kelava needlessly gave the ball away to Taye Taiwo whose cross was missed by Ideye Brown but rebounded off an unwitting Pivaric behind him and into the net.
Dynamo almost made it three before the break but Andriy Yarmolenko's shot from the middle of the area was parried away by Kelava.
The Croatians needed a goal quickly after the break and while Duje Cop drew an early save from Olexandr Shovkovskiy Dynamo quickly settled back into their dominance.
Yarmolenko and Gusev both forced Kelava into action while Veloso was twice off target as the hosts looked for the further safety of a third goal.
It never arrived but it matter not as Dynamo grabbed three points to move them level with second-placed PSG in Group A.