City should have been celebrating securing a place in the last eight for the first time but by full-time at the Etihad Stadium the mood seemed rather sombre, as the implications of the injuries sank in.
The loss of Kompany, with a tricky run-in ahead, could be particularly galling - although on this occasion his team-mates coped well enough without him to ensure progress courtesy of last-month's 3-1 win in Ukraine.
It was a largely dreary encounter that only spluttered into life when Yaya Toure attempted to force the issue in the second half, but the closest City came was when Jesus Navas hit the post.
Their night could hardly have got off to a worse start as Kompany pulled up yet again attempting an early clearance
He immediately slumped to the ground and the groan around the stadium was audible.
The Belgian's body language suggested the problem was serious and with just six minutes of the game gone he was limping off
Initial reports suggested he had suffered a calf injury and, if confirmed, it would be the 13th such problem since the start of the 2011-12 campaign and his fourth this season.
His importance to City in terms of influence and defensive ability cannot be understated - and the concerns with a derby against Manchester United coming up were obvious - and the problem was immediately compounded by an injury to Otamendi.
The Argentinian was hurt in a hefty challenge from Vitaliy Buyalskiy and his attempts to run off the knock - after being booked for re-entering the field without the referee's permission - proved unsuccessful
After aggravating the problem hitting a long ball he was removed and, with just 23 minutes gone, City had an all-changed centre-back partnership of Eliaquim Mangala and Martin Demichelis.
The disruption robbed City of any vitality and their first-half performance was one of the worst served up at Eastlands all season.
Their best moment came when Navas burst through the Kiev defence, brilliantly skipping one challenge, but the Spaniard then overhit his pass for Pablo Zabaleta and the crowd groaned again
Sergio Aguero did get in a shot but slipped in doing so and it curled well wide.
City were fortunate Kiev were not at their most potent either, although fans' nerves were hardly eased when a poor Demichelis pass played Mangala into trouble and Andriy Yarmolenko almost pounced.
Joe Hart also had to punch clear from a clear flicked header by Denys Garmash.
City woke up a bit after the break with Toure coming to the fore
He curled a free-kick over and then teed up Aguero and Navas, who shot across goal and hit the foot of the post respectively
He had another chance himself but picked out goalkeeper Olexandr Shovkovskiy while, at the other end, Yarmolenko shot straight at Hart.
Yarmolenko had a penalty appeal turned down and Hart saved from Olexandr Yakovenko as Kiev rallied late on but it hardly made the game much of a contest.
City had done their job, albeit at a cost.
Source: PA