A special police unit took the unidentified man into custody at Essen's central railway station on Wednesday evening on an arrest warrant issued against him by a district court in the city, police said.
A person accompanying him was also detained and kept in custody, it said in a press statement last night.
Police gave no further details, but media reports identified the third man arrested as jihadist Tolga I from Wesel in the state of North Rhine Westphalia, who gave the orders to the two main suspects to carry out the terror attack.
Sixteen-year-old secondary school students Mohammed B and Yussuf T were arrested four days after they allegedly detonated a fire extinguisher filled with explosives at the entrance of the Nanaksar Satsangh Sabha Gurdwara on the evening of April 16, as India expressed "distress" over the attack.
The strength of the Sikh community members in Germany is estimated around 15,000.
The two teenagers are currently in preventive custody.
A priest of the gurdwara was seriously wounded and two others suffered minor injuries in the blast which ripped through the entrance hall of the gurdwara at the end of a wedding ceremony.
Seventeen-year-old Tolga I met the two terror suspects in the Assalam Mosque in Essen just hours before they exploded the bomb, ARD TV network reported in its 'Report Muenchen' programme.
He had formed a twelve-member WhatsApp group in which the two main suspects are members, the report said.
Tolga I also has links to a group of jihadists in Dinslaken town and to the "Lohberger Brigade", a group of radical Islamists, who have joined the Islamic State terror group as fighters some years ago, it said.
Regional newspaper Westdeutsche Allgeneine Zeitung reported that Tolga I was already detained by police on April 20 on suspicion of involvement in the gurdwara attack, but suspicions against him could not be substantiated and he was set free.
Immediately after the bomb attack, Yussuf T had sent a message to Tolga I via WhatsApp about the operation, the report said.
The newspaper said Tolga I is known to police as an ISIS sympathiser and local authorities have placed a restriction on his travel abroad and impounded his passport because they feared he may join IS in Syria or in Iraq.
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