Jaber al-Bakr killed himself in a jail in Leipzig late on October 12, reportedly with his own T-shirt.
Justice Ministry spokesman Joerg Herold said 22-year-old Jaber al-Bakr killed himself some time in the evening, and the incident was being investigated.
The development adds to pressure on Saxony state authorities who had already been criticised for allowing Albakr to slip through their fingers as they prepared to raid an apartment where he had been staying in the city of Chemnitz on Saturday.
Albakr, who had been under surveillance by German domestic intelligence since last month, was observed exiting the apartment building and authorities fired a warning shot, but he eluded police at the scene and fled the city.
Inside the apartment officers found highly volatile explosives and a home-made bomb vest.
Albakr, who had been granted asylum after arriving in Germany last year, was finally arrested on Monday in the city of Leipzig after three fellow Syrians tied him up and alerted police.
Earlier on Wednesday, interior minister Thomas de Maiziere said Albakr had undergone a security check last year, but it did not turn up anything suspicious.
“There was a check against security authorities’ data in 2015, but without any hits,” he said. “It’s not clear when he was radicalised.”
German authorities have said they believe he had links to Islamic State and was thought to be planning to attack a Berlin airport, possibly as soon as this week.
German media have reported that after his initial arrival, Albakr returned to Syria through Turkey and then came back to Germany. Mr de Maiziere said that was part of the investigation and would not comment.
Federal prosecutors also refused comment.
The three Syrians who captured the suspect have already been granted asylum, Mr de Maiziere said in response to calls for their applications to be fast-tracked due to their heroism.
He said their “behaviour deserves praise and recognition”.