It ends any lingering hope Owen had of being involved in England's final two qualifiers against the Ukraine and Belarus next month.
And, given Fabio Capello was at Old Trafford to witness Owen limping off after just 20 minutes of United's 2-1 Champions League win over Wolfsburg, there must now be a huge question mark over the 29-year-old forward's ability to force his way into the Italian's plans before England head to South Africa next summer.
"Michael felt a slight groin injury after training on Sunday," revealed Ferguson. "He thought he was fine to play but on a wet surface, when he tried to turn quickly, it came back again.
"It is not a serious one and I am not worried because players do get them, but he will be out for two to three weeks.
"The only good part is that his fitness levels are very good."
If it was a night of misery for Owen, it was another night of glory for Ryan Giggs. With a banner at Old Trafford now demanding a knighthood for the veteran Welshman, it is hard to see how much more praise there is for the reigning PFA player of the year.
Having scored his first United goal with the aid of a massive deflection in 1991, it was somehow fitting he should become the ninth Red Devil to reach 150 in the same manner. His free-kick was on target but probably would not have troubled Wolfsburg keeper Diego Benaglio until it smacked into the wall and ended up in the bottom corner.
"All Ryan is doing at the moment is continuing to play," reflected Ferguson. "The amazing thing is he shows this incredible youthfulness about his performance. It is as if he has just started his career. You can give him as many as you like, he doesn't get affected by it, which is good. What more can you say? He is continuing like a young man. He is enjoying his football, which is wonderful to see."
It should have been no surprise either than Giggs should supply the final pass for Michael Carrick's matchwinner 12 minutes from time.
In truth, it was a minimal contribution, the veteran Welshman pushing a pass for Carrick, whose splendid first-time finish gave Benaglio no chance. The goal – Carrick's first of the season – gave United a clear advantage in Group B, with just a win and a draw required from next month's double-header against CSKA Moscow to hit the ten-point target Ferguson always sets for qualification.
Amid the euphoria of victory, Ferguson could not have helped but notice the impressive performance of Edin Dzeko, the 23-year-old Bosnian, who is surely destined for greater things. Dzeko put the visitors in front with a towering far-post header and was a constant threat to United's experienced back four.
Man Utd: Kuszczak, O'Shea, Ferdinand, Vidic, Evra, Valencia (Fletcher 82), Carrick, Anderson, Giggs, Owen (Berbatov 20), Rooney. Subs not used: Foster, Brown, Nani, Scholes, Fabio Da Silva. Booked: Vidic.
Wolfsburg: Benaglio, Riether, Madlung, R Costa, Schafer, Josue, Hasebe (Ziani 73), Misimovic, Gentner, Dzeko, Grafite (Martins 82). Subs not used: Lenz, Santana, Pekarik, Dejagah, Barzagli. Booked: R Costa.