The Blues were held to a 0-0 draw by Dynamo Kyiv but progress to the last eight after winning 3-1 on aggregate.
The triumph, however, was soured by the loss of Captain Vincent Kompany after just eight minutes after he pulled up sharply as he cleared the ball.
Within 15 minutes, central defensive partner Nicolas Otamendi had also limped off after a heavy collision meaning Martin Demichelis and Eliaquim Mangala had both come on with just 23 minutes on the clock.
With the Manchester derby looming, the Blues’ injury jinx seems to have struck yet again.
The first-half was something of a non-event with City well aware it was the visitors who had to chase the game.
The Blues recalled Yaya Toure and Pablo Zabaleta to the starting line-up but lost Kompany with who seemed to know the moment he cleared a ball down the right flank.
It was a bitter blow for both the skipper and City following a series of set-backs for the Belgian this season who looked as crestfallen as everyone else inside the Etihad.
Otamendi went soon after following a powerful challenge on the halfway line that he initially attempted to run off before finally limping off.
The teams reached the halfway point with neither goalkeeper seriously tested in a fairly uneventful 45 minutes.
City were more inventive after the break and almost went ahead on 61 minutes when Jesus Navas saw a low drive cannon off the inside of the post and moments later Andriy Yarmolenko cut inside the Blues’ box but fired his shot straight at Joe Hart.
Yaya Toure then hit a free-kick a few feet over the bar and had another chance on 72 minutes but his low shot from Navas’ cross was easily saved by the 41-year-old Kyiv keeper Olexandr Shovkovsky.
Sergio Aguero received one of the loudest cheers of the night on 77 when his cheeky back-heel left two Kyiv defenders chasing his shadow but his pass to Silva as he raced into the box was too close to the keeper.
Kyiv threatened in the last few minutes and should have won it with the last kick of the game but Hart denied Olexandr Yakovenko from point-blank range as the Blues recorded back to back goalless draws.
It wasn’t a thriller, but job done and now City await to discover their quarter-final opponents on Friday’s draw.