In fairness, O'Neill's 'second-string' side were far from disgraced on the plastic pitch of the Luzhniki Stadium on Thursday as the line-up shorn of its stars only succumbed after an hour.
It was at that stage Yuri Zhirkov thundered an edge-of-the-area drive beyond an otherwise exemplary Brad Guzan.
Even then Villa were far from out of the equation in the second leg of this last-32 tie, and it was only in the third minute of injury-time that Vagner Love put the game beyond doubt.
This match, though, will be remembered for the fact O'Neill opted to keep Gareth Barry, Brad Friedel, Emile Heskey, James Milner, Ashley Young, Gabriel Agbonlahor, Carlos Cuellar and Stiliyan Petrov at home.
The aim is qualification for next season's Champions League, and only come mid-May will O'Neill know if a decision he rates as the hardest in his time as Villa manager will be justified.
"I'm disappointed we've gone out of the competition," said O'Neill about a side which included 19-year-old youngsters Barry Bannan and Marc Albrighton making their full debuts.
"But we've played a lot of games this year, 11 or 12 more than we did throughout the whole of last season.
"It's not a decision that was taken lightly, and if I had thought of playing just young players then we would not have travelled here on Tuesday, stayed the three nights and gone back on Friday.
"Circumstances forced me into making my decision, and whilst I am disappointed we were beaten, I will have to see what the rest of the season brings to see if that disappointment is worsened."
O'Neill's message is that the season is far from over, adding: "We have played very strongly this year and that's why we are in the position we're in, and we don't want to give it up lightly.
"Given another opportunity, something this football club should be able to obtain, I think the experiences we've had, from July (the Intertoto Cup) through to now, will stand this team in good stead."
One of the few positives for O'Neill were the performances of Bannan and Albrighton, who operated on the right and left wings respectively.
"We had two players making their first starts in wide positions and I thought they did exceptionally well," added O'Neill.
"We were always in the game until the last minute, and we always felt we were capable of scoring a goal, and we had one or two opportunities to do so.
"We have tried our utmost, but it was not to be."
Villa barely conjured a chance worthy of the name, and although their work-rate cannot be faulted, CSKA were hardly troubled.
Brazil legend Zico, in his first competitive game as manager of CSKA on home soil, was happy enough his side had progressed.
"I am satisified with the game," remarked Zico.
"We had an overwhelming advantage, and I am delighted we've managed to get through to the next round.
"The two games were a challenge against a Villa team doing well in the Premier League, but our professionalism and the high quality of our players managed to overcome any difficulties."