Haikel Saydani, 37, "has been handed over to the authorities there," said Hesse interior minister Peter Beuth.
The expulsion paves the way for Germany to also deport Osama bin Laden's former guard, named only as Sami A., likewise a Tunisian who has argued against his return over the threat of torture in his country of origin.
Following Saydani's expulsion, Interior Minister Horst Seehofer said he "aimed to achieve the deportation as well in the case" of Sami A., who lives in Bochum.
Saydani was arrested in February 2017 in Hesse during an anti-terror raid.
German investigators accuse him of building an Islamist network in Germany for a possible attack.
In Tunisia, Saydani is also accused of participating in the 2015 attack at the National Bardo Museum in Tunis that killed 21 foreign tourists. The assault was claimed by Islamic State group militants.
On Monday, German judges threw out Saydani's appeal, finding that he did not face the threat of the death penalty as Tunis has had a moratorium on implementing capital punishment since 1991.
On the same day, he lost a last-ditch bid for a stay at the European Court of Human Right.
Beuth said the expulsion showed that "despite the lengthy process, it is possible to expel foreign criminals and dangerous Islamists".
The case would "hopefully greatly shorten the length of the (expulsion) process," he added.
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