The club, who finished second in the SAS Ligaen this season, wanted to keep the defender for another year, but could not agree terms with the League One champions.
Former Wolves manager Stale Solbakken, who is now in charge of FC Copenhagen, told the Express & Star: "We tried to keep Margreitter, but it was far from successful. He has a very good contract at Wolverhampton, which is far from our level so we could not meet his demands.
"He's a rock-solid man on and off the field who has proved worthy of the role we loaned him to fill. But a dialogue with Georg and Wolverhampton has shown it's so difficult to negotiate a loan extension, so now he must return to England and be Wolves' player.
"Georg is growing, and, with the playing time he's had in the last few months, he's shown his true potential."
Solbakken was in charge at Wolves when the club signed the 25-year-old from Austria Vienna.