Authorities first sought two men from Bonn's militant Islamist scene, who had previously been classified as "dangerous."
Omar D. and Abdirazak B. were arrested on Tuesday afternoon, security forces in Berlin confirmed, but have since been released.
Somali-born Salafist Muslim Omar D., had been taken into custody at Cologne/Bonn airport in 2008 on suspicion of engaging in terrorist activities. Omar D.'s lawyer Mutlu Günal also confirmed the arrests, but refused to comment further.
The police investigation came after a sports bag was found on Platform 1 of Bonn's central station on Monday. Der Spiegel magazine reported that it contained four canisters of butane gas, ammonium nitrate, a metal pipe, and an alarm clock with batteries, though there appears to have been no detonator.
The area was sealed and the device was destroyed with a water cannon - which may have broken the detonator into "countless pieces," prosecutors said.
But authorities said that if the explosive had been detonated, it could have had a similar effect to the 2004 al-Qaida bombing in Madrid, which killed 191 people.
"It was an extremely dangerous explosive device," state prosecutor Rainer Griesbaum said on Wednesday.
Yet it remains unclear whether the crime was politically or criminally motivated. "In one word - everything is open," Griesbaum said. Investigators believe that the bomb was not meant to be left in the railway station, but perhaps deposited on a train.
Police said they are continuing their investigations, and are searching for a 30-35-year-old dark-skinned man with a slim build and around 1.90 metres tall, who was seen leaving the bag by a 14-year-old boy. The suspect was reportedly wearing a black hat, black boots, and a brown and grey jacket.
CCTV footage taken from a McDonalds restaurant near the station appears to show the bag being carried by a white man before being taken away by a black man. Investigators are unsure whether this was an intended "drop" or a theft.