The two men and a woman were sent back to Poland from a train station in the eastern city of Frankfurt an der Oder on Germany's eastern border on the grounds that they had sought to enter from a safe third country, a court statement said.
The ruling could challenge the tougher migration stance by Chancellor Friedrich Merz's conservative-led coalition, which was elected in February promising a crackdown that has caused concern in neighbouring countries.
It is the first such case since Merz was elected, RBB media said, citing a court spokesperson.
"The rejection of the applicants was unlawful," the Berlin court said in a statement, explaining that their asylum application should have been processed by Germany under the European Union's so-called Dublin rules that determine which country is responsible for processing an asylum application.
"However, the applicants could not demand to enter the Federal Republic of Germany beyond the border crossing," it added, saying that the application could be processed at or near the border.
Migration is among German voters' biggest concerns and a backlash against an influx of new arrivals has contributed to a rise in support for the populist nationalist Alternative for Germany party, which came second in a federal election in February.
It is a profound shift since Germany's "Refugees Welcome" culture during Europe's migrant crisis in 2015 under Merz's conservative predecessor Angela Merkel.
Merz's government issued an order in May to reject undocumented migrants, including asylum seekers, at Germany's borders.
Monday's ruling was seized on by the Greens party, now in opposition, which said it vindicated their stance that Merz's migration crackdown was unworkable.
"This is a severe defeat for the federal government and should serve as a warning to abide by the law in the future and not knowingly exceed its own powers for populist purposes," Greens MP Irene Mihalic told the Rheinische Post newspaper.
"The border blockades were a rejection of the European Dublin system and have offended our European neighbours."
Interior Minister Alexander Dobrindt said last week he hoped the European Union can reach a bloc-wide agreement allowing for failed asylum seekers who cannot go home to be sent to safe countries near their original homelands.
Karl Kopp, managing director of pro-immigration advocacy group Pro Asyl, told the Rheinische Post: "Dobrindt's unlawful practice of national unilateral action in asylum policy has failed. This nonsense must now come to an end."
He called for the three Somalis to be able to re-enter Germany.
The European Commission, the EU's executive body, proposed a scheme last month that would let member states reject asylum applications by migrants who passed through a "safe" third country on their way to the bloc.
The proposals, criticised by rights groups, have yet to be adopted by any member governments or the European Parliament.
