Investigators accused the 33-year-old German doctor of brainwashing the 24-year-old man with jihadist videos and later paying for his one-way ticket to Syria and Iraq.
The younger man, also a German national, subsequently blew himself up in northern Iraqi city Baiji, killing at least 12 Iraqi soldiers, said prosecutors in a statement.
"Findings by investigators showed that the suicide bomber was mentally restricted and easily influenced and had therefore been assigned a carer," prosecutors said.
"Whether the attacker was deliberately singled out by the accused because of his mental deficiency is the subject of further investigations," they added.
The Berlin arrest came during raids of four apartments in the German capital and the southwestern city of Mannheim, where police seized an optical device for a firearm, documents, mobile phones and electronic data storage devices.
Thousands of Europeans have travelled to Syria to fight for the IS group, and concern is growing over the threat these jihadists pose on home soil when they return home.
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