United looked comfortable after taking the lead thanks to an own goal from Sergio Ramos early in the second half.
But just before the hour mark Nani was shown a straight red card for a high tackle on Alvaro Arbeloa.
United were then pegged back by the Spaniards as they went in search of the goal that would level things up.
Luka Modrić and then Cristiano Ronaldo both found the net within three minutes of each other, and that proved to be enough to take Real into the last eight of the competition.
Cakır has come under criticism for his game-changing decision, but Owen can understand why the Turkish official decided to show Nani the red card.
Owen wrote on his Twitter page: “Plenty of fallout from last night’s game. Main talking point that changed the tie was the sending off. It’s all about interpretation.
“Endangering the safety of a player is a sending off according to the rule book. You have to say that the challenge did fall into that category. Not in a million years would we see a red card for that in the Premier League but on the continent it’s a definite red.
“Can’t really blame the referee for it as he is obliged to play to the rules but it’s a hard one to take bearing in mind there was no intent.
“The rule book is the same throughout the world. I wouldn’t have sent him off if I was the referee but again, it goes back to interpretation."