Police detained the 20-year-old German man of Turkish origin and a German-Iraqi woman, 33, on a train in Rosenbach in Austria on Saturday, police in southern Germany said.
Prosecutors in Munich had issued arrest warrants for the pair amid a police inquiry into the suspected preparing of a grave seditious act of violence, the city's police said in a statement.
The Munich pair, named as Samil A. and Farah H., are alleged to have travelled to Syria in August "and joined there the armed fight by jihadist groupings", it said.
"It is also notable that the woman also took her eight-year-old son on the trip to the crisis region," it added.
The pair, who were married under Islamic but not German law, are being held for extradition and the child initially placed in a youth care centre in Austria.
reported that they spent two months in Syria. Samil reportedly posted photos on his Facebook profile, which has now been taken down, of him in military uniform with a Kalashnikov.
Police in Germany have also arrested a man on charges of belonging to a foreign terror organisation during an extended trip to Syria, officials said earlier on Thursday.
The 27-year-old German national, identified as Soufiane K., is alleged to have been a member of the Al-Qaeda-backed militant group Al-Nusra Front, the federal prosecutor general in Karlsruhe said.
He allegedly left his western German home in Rüsselsheim for Syria in July 2013 and later joined the group, a statement said.
He is suspected of having received combat training and carried out guard duty for the militant group, among other things, it added.
The man returned to Germany in June, the federal prosecutor general said, adding that since then, suspicion of his involvement with Al-Nusra Front had grown leading to an arrest warrant.
The suspect was due to appear before an investigating judge on Thursday.
Concerns are mounting in Europe about the growing national security threat posed by jihadists returning from war-torn Syria and Iraq.