The striker scored for new club Palermo on Sunday but also picked up a knock and, due to the short turnaround time, has not been able to join his international team-mates in Belfast.
Lafferty is an automatic pick when fit and available, with O'Neill valuing his physicality and ability to lead the line on his own.
Those attributes would have been a central part of O'Neill's strategy against a hotly-fancied Russian side managed by Fabio Capello, but he must now decide how best to cover the 25-year-old's absence.
Brentford's Will Grigg is the closest to a like-for-like replacement but has just two caps and has yet to start a competitive fixture, while Aberdeen's Josh Magennis is another option having been added to the squad on Tuesday.
More likely, though, is a different brand of centre forward - with the Huddersfield's Martin Paterson, Derby's Jamie Ward and Billy McKay of Inverness the other options available.
O'Neill may yet opt for a combination of two, but he admits that with Lafferty joining Chris Brunt (suspended) and Chris Baird (unattached) in missing the fixture, he has been left with gaps to fill.
"It's disappointing that Kyle isn't in the squad but we were always going to be under pressure with players playing on the Sunday," said O'Neill.
"He has an Achilles tendon injury which we hoped would have settled in the past 24 hours but it hasn't and unfortunately he is unavailable, but it will provide an opportunity for someone else to come in.
"One of the other strikers - Martin Paterson, Will Grigg, Josh Magennis - there is a number of options.
"We have played Paterson through the middle and his best position is as a lone striker, so it's a different option in terms of the players we have there, and we also have Jamie Ward back who we haven't had for a while.
"But to be without Kyle, Bairdy, Chris Brunt... that's a blow. They are big players for us.
"There are many things in international football which are beyond our control."
O'Neill has yet to experience a victory on the international stage, having drawn five and lost four of his nine games at the helm.
The arrival of a Russia side with four wins from five Group F outings and the experience of Capello on their side is hardly the ideal opportunity to end that sequence, but O'Neill insists that is the target.
Fans at Windsor Park have been increasingly restless following draws with Luxembourg and Azerbaijan, as well as a 2-0 defeat to Israel last time out, and the manager is eager to give them something to smile about.
"My expectation will be to give a competitive performance and show ourselves as an organised team," he said.
"We have been away to Russia and Portugal so the expectation will be to take something from the game.
"Our approach will be to win. I think the crowd have been great, when you look back to the Azerbaijan game they were with the team right through to 93rd minute and Israel, I think there was stunned silence when we lost the goal as we dominated large portions of the game.
"It's a two way thing, the players have a responsibility to get the crowd into a singing mood and equally if that's done, then the players will respond. Hopefully there's not a fear factor for them and they come into an atmosphere."
O'Neill has no other fitness concerns, with Manchester United defender Jonny Evans expected to start despite remaining on the bench during the Community Shield having suffered a pre-season niggle.
Russia manager Fabio Capello has continued to ignore the claims of experienced pair Andrey Arshavin and Roman Pavlyuchenko for the match and is also without Alexander Kokorin (heel), Alexei Berezutsky (collarbone) and former Yury Zhirkov (hamstring).