Leading 3-1 from last month's away leg, Manuel Pellegrini's side completed the job in forgettable fashion, with Jesus Navas's shot against the post for City the nearest either side came to breaking the deadlock.
But first-half injuries to captain Kompany and Otamendi cast a pall over the evening at a hushed Etihad Stadium, leaving City vulnerable in defence ahead of Sunday's derby with Manchester United in the Premier League.
"It is a very important achievement for the club. This is a club that is growing and continuing to develop as a big club," said Pellegrini.
"Vincent unfortunately has another muscular injury in his calf, which he has had before. We'll know tomorrow (Wednesday) or after tomorrow how serious it is. Usually with muscular injuries, minimum a month.
"Otamendi has an important kick and can hopefully recover in the next couple of days."
While progress in the Champions League represents a historic achievement for Pellegrini, who will hand over to Pep Guardiola at the season's end, the injuries could have a costly impact on City's attempt to resurrect their domestic title challenge.
The League Cup winners have fallen 12 points below leaders Leicester City, although they retain a game in hand, and face challenges from both United and in-form West Ham United for their top-four place.
Pellegrini welcomed Yaya Toure back from the heel problem that had caused him to miss Saturday's frustrating 0-0 draw at Norwich City, but within seven minutes he was counting the cost of another injury.
After misjudging a bounce on the City right, Kompany slipped as he tried to recover the situation and immediately realised that he had done himself damage, passing the ball out of play and signalling to the bench before limping off with a look of disgust etched on his face.
The Belgium international, who has suffered 14 calf injuries since 2008, was soon joined in the home changing room by Otamendi, who came off second-best in a collision with Vitaliy Buyalskiy.
- Aguero miscues -
The Argentine attempted to play on, before admitting defeat, leaving City with reserve centre-backs Eliaquim Mangala and Martin Demichelis in the heart of their defence.
It was not a combination that will have inspired great confidence among the home support and there were early nerves as Mangala's missed kick from Demichelis's pass almost let Lukasz Teodorczyk in on goal.
With the atmosphere affected by the double injury blow, City struggled to get going and when Navas managed to pick Sergio Aguero out with a right-wing cut-back, the Argentine miscued.
Visiting goalkeeper Olexandr Shovkovskiy was not tested until early in the second half, when he showed a neat touch to control the ball on his thigh after a defender had inadvertently prodded it towards his own goal.
City began to show signs of life, Toure curling a free-kick over the bar and Aguero dragging a shot wide, before Navas collected a pass from Toure and drilled a low shot against the left-hand upright.
Moments later, City goalkeeper Joe Hart made his first save of the night, comfortably fielding an effort from Andriy Yarmolenko after the Ukraine winger robbed Gael Clichy.
Toure continued to drive the home team forward and he threatened to make the breakthrough from Navas's cut-back, only for Shovkovskiy to save.
There were two late scares in the hosts' box when first Buyalskiy and then substitute Olexandr Yakovenko took aim, but Hart blocked alertly on both occasions, giving City a clean sheet for only the second time in their 18 Champions League home games.
"We had chances to score and Manchester had chances to score," said Dynamo coach Sergiy Rebrov.
"The guys showed they deserved to be in the Champions League. This game was a good experience."
source: www.abs-cbnnews.com
