Police launched a probe into possible human trafficking after they were tipped off about the advertisement which appeared online for around 30 minutes on Tuesday.
The 40-day-old girl has been handed to child protection officers, police from the western city of Duisburg said in a statement.
Police raiding the couple's apartment also took away material potentially serving as evidence.
Preliminary investigations show that the advertisement was put up using the internet connection of the couple, identified by police only as "refugees".
However, police said the internet connection was also in use by other members of the family, adding that the probe was ongoing.
Bild daily reported that the online connection was not secured and could be used even in the neighbouring apartments.
"That's why other witnesses will have to be questioned," said the tabloid, adding that the baby is the couple's only child and that they have been in Germany for a year.
When questioned by police, the 28-year-old father and 20-year-old mother reportedly confirmed that the photos posted online were of their baby.
Several pictures of the black-haired infant were seen in the advertisement, which was titled "40-day-old child named Maria ...for sale."
An eBay spokesman told national broadcaster ZDF that employees from the company had alerted authorities after noticing the advert.