Acting on information from Interpol, authorities arrested Jihad Hamad, 19, in the northern city of Tripoli on Thursday morning, the officials said, speaking on condition of anonymity because they were not authorised to talk to the media.
German officials had reported that Hamad turned himself in to Lebanese authorities.
Hamad was later taken to Lebanon's anti-terrorism centre in Beirut for interrogation, the officials said.
Hamad is the second main suspect held in the failed plot to bomb two German trains last month.
Acting on tips from Interpol, Lebanese anti-terrorism police had searched for Hamad for about a week in northern Lebanon.
They went on Wednesday to Hamad's house in the northern city of Akkar but he was not there, the officials said.
Instead, they spoke to his father who told the police he did not know his son's whereabouts.
Later, Hamad was lured to Tripoli where he was arrested on Thursday morning, the officials said without elaboration.
The other main suspect, a 21-year-old Lebanese student identified as Youssef Mohamad el Hajdib, was arrested in Germany last weekend.
The two are accused of planting bombs that failed to explode on two regional trains on July 31.
An international arrest warrant was issued on Wednesday for Hamad on suspicion of membership in a terrorist organisation, attempting to set off an explosion and multiple counts of attempted murder.
Authorities have said others possibly were involved in the plot, and the German prosecutors said in a statement that the investigation continues.
German prosecutors said they would attempt to have Hamad, who lived in Cologne, extradited to Germany.