Sir Alex had already been left to rue injuries to Wes Brown and Gary Neville in the weekend victory over West Ham United, while Nemanja Vidic did not travel with the rest of the squad for the Champions League clash with Vfl Wolfsburg.
Evans has a calf injury which O'Shea's problem was not revealed.
Injuries forced Sir Alex to finish the 4-0 win at Upton Park with midfielder Michael Carrick and lef-back Patrice Evra as the centre-back pairing. Ryan Giggs had to fill in on the left of defence with Darren Fletcher on the opposite flank.
United had hoped Vidic would have recovered from the flu bug that kept him out of Saturday's win at West Ham. However, the Serbian was absent as the Red Devils checked in for the short flight to Germany, giving their manager a major headache.
His list of injured defenders includes skipper Neville and England international Brown, plus longer-term casualties Rio Ferdinand, O'Shea and Evans. With the Da Silva brothers, Fabio and Rafael, also sidelined, the only orthodox defender Ferguson has in his squad is Evra.
Ferguson has already revealed his intention to play Michael Carrick in central defence again, while Fletcher seems certain to occupy a defensive berth, too, although which one is open to debate.
Among the less familiar faces in the United party are Oliver Gill, son of chief executive David, Magnus Eikrem, Cameron Stewart, Matte James and Oliver Norwood.
Normally, Ferguson would only class outings such as this as useful staging posts in a young player's development. However, on this occasion, there is the very real possibility they could play a prominent part.
Ferguson has vowed not to give preferential treatment to Gill. "It doesn't concern me. If he is good enough, he plays,'' said Ferguson. "That is the name of the game at Manchester United. I had my own son in the squad for four or five years and he was treated exactly the same as any other member of the squad. It will be the same for Oliver.''
Of the crisis which leaves the United boss with just one experienced defender, Sir Alex said: "One defender. It is worth trying. It would be easy to organise anyway.
"Wolfsburg will be delighted we have so many injuries. I know we might come second in the group but I am not sure whether it really makes much difference. AC Milan and Real Madrid are in one group, Bordeaux, Bayern Munich and Juventus are in another, Barcelona, Rubin Kazan and Inter Milan in a third, so if you get one of those it doesn't matter whether you have finished first or second.
"The one issue is that if you finish second you have to play the first leg of your knock-out round at home but that is all.''
In addition to the defensive problems - first-choice keeper Edwin Van der Sar is also missing - Ferguson has taken the option of leaving Wayne Rooney and Dimitar Berbatov at home, meaning Michael Owen and Danny Welbeck are the only strikers in his 19-man squad.
Given Wolfsburg are unbeaten at home in this season's competition, it would appear United's best hope of finishing top would be for CSKA Moscow to beat Besiktas in Istanbul, which would leave the Red Devils at the head of affairs no matter what their result.
At least it should mean Paul Scholes should retain his place for a game the former England star feels will round off what has been a harder group than seemed likely when the draw was made.
"This was one of the toughest groups,'' he said. "We had to go to Moscow, which is always difficult, especially on a plastic pitch, and it is the same in Turkey, yet we managed to win both games.
"CSKA and Besiktas went on to prove at Old Trafford that they are very capable teams and, when you take into account Wolfsburg are the German champions, we did well to qualify as early as we did.''
He continued: "We want to win the game and finish top of the group. How much difference that makes to who we get in the next round, I am not too sure. There are lots of good teams at that stage of the tournament."