Owen headed home Nani's cross on the stroke of half-time, and after Wolfsburg rallied through Edin Dzeko on 56 minutes the nimble forward slotted home seven minutes from full-time and sealed the win with a crafty finish in added time to send the English champions through as Group B winners.
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Injury-hit United, fielding just one recognised first-team defender in French international Patrice Evra, rode their luck at times, although Wolfsburg only had themselves to blame for failing to take several excellent chances against United's makeshift defence which featured regular midfielders Michael Carrick and Darren Fletcher.
A decent penalty claim was dismissed early in the first half when Makoto Hasebe was upended by Carrick, while Andrea Barzagli and Zvjezdan Misimovic missed excellent chances.
Defender Barzagli nodded a free header from four metres out well over the bar and following a flowing move forward Misimovic wasted another free header at the back post.
Lacklustre in the first half, Wolfsburg were transformed in the second period and played with more purpose after the wake-up call from Owen, but it was the England man who had the final say.
Wolfsburg's consolation is a Europa League last 32 knockout stage place after finishing third in the group.
United manager Alex Ferguson was delighted after Owen's match-winning performance.
"Fantastic. Brilliant. You know what he is. His timing of runs is fantastic," he told Sky Sports.
Owen moved to United in July from Newcastle United.
