The 42-year-old, identified only as Sami A., should be brought back to Germany, the administrative court in Gelsenkirchen ruled on Friday evening, just hours after news broke he had already been deported to Tunisia.
The court said Sami A.'s deportation had been “grossly unlawful,” Die Welt newspaper reported, because Germany had received no guarantees from Tunisia that he would not be tortured on arrival.
Sami A. had lived in Germany for more than two decades, but outrage over his presence grew in recent months as Germany cracks down on failed asylum seekers.
News had broken earlier on Friday of his deportation.
“I can confirm that Sami A. was sent back to Tunisia this morning and handed over to Tunisian authorities,” interior ministry spokeswoman Annegret Korff told reporters, following a report in the top-selling Bild newspaper.
Sami A. had previously successfully argued against his deportation, saying he risked being tortured in his homeland.
A court in the city of Gelsenkirchen ruled against the deportation late Thursday, upholding the assessment that the suspect potentially faced “torture and inhumane treatment”.
However the decision only reached federal authorities – by fax – on Friday morning, after Sami A.'s flight to Tunisia had taken off, DPA news agency reported.
Considered a security threat over his suspected ties to Islamist groups, Sami A. has for years had to report to police but was never charged with an offense.
He has always denied being the former bodyguard of late Al-Qaeda leader bin Laden, the mastermind behind the 9/11 attacks on the United States.
Judges in a 2015 terror case in the German city of Muenster however said they believed Sami A. underwent military training at an Al-Qaeda camp in Afghanistan in 1999 and 2000 and belonged to bin Laden's team of guards.
German authorities first rejected Sami A.'s asylum request in 2007 but prosecutors' efforts to expel him were repeatedly blocked by courts citing the danger of torture in Tunisia.
An unrelated court ruling last month involving another Tunisian man – accused over a 2015 attack on Tunis' Bardo museum – helped pave the way for Sami A.'s expulsion.
In that instance, German judges found that the accused did not face the threat of the death penalty as Tunis has had a moratorium on implementing capital punishment since 1991.
Germany's hardline interior minister, Horst Seehofer, seized on the precedent to say he hoped Sami A. would be next, calling on migration officers to make the case “a priority”.
Bild led a vocal campaign against Sami A.'s presence in Germany, with revelations that he collects nearly 1,200 euros ($1,400) a month in welfare sparking particular outrage.
Sami A. has a wife and children who are German citizens.