Jose Mourinho’s side were already assured of progress in Europe prior to a trip to Valencia on Wednesday.
They could, however, have topped Group H had they taken maximum points from that contest, with Juventus suffering a surprise 2-1 defeat to Young Boys.
United came unstuck by the same scoreline on Spanish soil, with another disjointed display seeing Phil Jones put through his own net and the Red Devils make little impression in the final third until Marcus Rashford grabbed a late consolation.
Owen believes the performance sent out a worrying message to the rest of the continental elite, telling BT Sport: “The really sad thing is the group winners are probably looking at the runners-up and thinking Atletico Madrid and Liverpool are the ones to avoid.
“Manchester United, as much as it still says Manchester United on the shirt, it’s just not the same Manchester United as it was six years-plus ago now.
“It’s been a pale shadow of that team for a long time now.
“They’re not the force to be reckoned with as they used to be.
“If they played next week I think they could beat Porto but I’d be very, very worried against anyone else.
“The good thing for Manchester United is there’s a couple of months now to regroup.
“At the minute, against any of those big boys, I couldn’t see them going through over two legs.
“The team just doesn’t reflect Manchester United teams that have gone deep in the competition on a regular basis.”
Prior to turning their attention back to European matters, though, Mourinho’s men have a crunch Premier League clash with arch-rivals Liverpool to take in on Sunday.