The suspects were identified only as 47-year-old German-Lebanese citizen Mahmoud El A. and 34-year-old Syrian national Akram O., the federal prosecutor`s office said in a statement.
"They are strongly suspected of regularly spying on Syrian opposition figures in Germany for the Syrian intelligence service for several years," it said.
The prosecutor`s office said around 70 federal and state police officers searched their homes and those of another six suspects.
The two suspects taken into custody will appear before a judge Wednesday who will present them with the arrest warrants dating from January 31.
German Foreign Minister Guido Westerwelle summoned Syria`s ambassador to Berlin following the arrests.
"Such actions against Syrian opposition members are utterly unacceptable," Westerwelle told reporters, referring to the spying charges.
In late December, a Berlin local politician active in the Syrian opposition was attacked by two men in his home in a case the German foreign ministry said it was following closely.
His party, the Greens, said it suspected the Syrian secret services were behind the assault.
No suspects have been identified in the case. (*)
Editor: Kunto Wibisono
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