The 21-year-old man remanded in custody by an investigating judge in Karlsruhe on charges of attempted murder, belonging to a terrorist organisation and attempting to cause an explosion.
The man, who was identified as Jussuf Mohammed E.H., was arrested on Saturday in a police swoop on the railway station in Kiel as he tried to flee the northern city, where he was a student.
He was flown from there to Karlsruhe by helicopter, handcuffed and in overalls.
According to the federal prosecutor, the man's fingerprints and DNA were found on one of the two suitcases in which homemade bombs were planted on trains travelling through Dortmund and Koblenz on July 31.
The bombs consisted of gas canisters, alarm clocks, wires, batteries and soft drink bottles filled with a flammable liquid and had been timed to detonate 10 minutes before the trains arrived at the stations.
The bombs failed to explode because of a technical error, but if they had, the trains could have turned into "balls of fire".
The judge heard that the two suspects met at the station in the south-western city of Cologne three weeks ago, where they boarded trains respectively bound for Dortmund and Koblenz.
Photos of suspects
They left the suitcases on board and got off before the bombs were timed to explode simultaneously at 2:30 pm (1230 GMT).
German media continued to run photographs of the suspects, both young men with dark hair, captured on closed circuit television cameras at Cologne station.
The pictures led to the arrest of the first suspect, and police hope it can also help them to snare the second.
Little is known about him, except that he is foreigner, about 20 years old and does not live in Kiel.
The prosecutor's office said police have searched the student dormitory in Kiel where the arrested suspect lived and a neighbouring property, but found no explosives.
A note in the case found in Koblenz contained Arabic writing and a Lebanese telephone number, and packets of starch with labels in Arabic and English were also found.
The head of the Federal Crime Office, Joerg Ziercke, has said the police have not ruled out that the planned attacks could have been motivated by the situation in the Middle East.