Waving banners and balloons marked with the slogans of the anti-nuclear movement, they turned out in force to protest outside Chancellor Angela Merkel's offices.
The organisers - environmental groups backed by left-leaning opposition parties - put their numbers at 100,000, though police estimated a figure near 40,000. Special trains and 150 buses had been chartered to bring the demonstrators to Berlin from all over Germany.
Merkel's centre-right coalition on Sunday agreed to lift the deadline of 2022 for the phasing out of nuclear power set by an earlier Social Democrat-led government. The new plan would extend the lifetime of Germany's 17 nuclear reactors for an average of 12 years beyond the previously scheduled shutdown.
Calculations in the German media suggest that the last plant will not be switched off until 2040, and critics say that operators may get away with keeping some running for even longer than that.
"It's a disgrace. We feel cheated," Hartwig Bottcher said, a 66-year-old retired teacher.
"During this time the pile of nuclear waste increases and we still don't know what to do with it," said 19-year-old student Laura, preferring not to give her full name.
"The government has gone down on its knees to the nuclear giants," said 33-year-old Claudia Schultz, who made the trip from Rostock in the north to protest with her two young children.
The government says the plan is necessary to maintain electricity supply until other renewable energy resources become available.
Even if the extension becomes law, the opposition Social Democrats (SPD), co-authors with the Greens of 2000's decision to exit nuclear power, said they will reverse Merkel's changes if they return to office.
With no permanent storage site for radioactive waste in place and fears about a repetition of a disaster in Germany like the Chernobyl meltdown in Ukraine in 1986, polls indicate a majority of voters oppose an extension.
Sociologist Klaus Hurrelmann said the wave of anti-nuclear sentiment could be "the match capable of sparking a new political movement," in the daily Neue Osnabrücker Zeitung.
The agreement with the energy companies is "scandalous" according to Jochen Stay, spokesman for the association Ausgestrahlt, or Irradiated, who hoped the protest on Saturday was only "the beginning of what will happen this autumn."
A load of Germany's nuclear waste is due to return from a French reprocessing facility in November and large protests are expected.
The international organisation Attac said the agreement was "about allowing RWE, EON, EnBW and Vattenfall to increase their huge profits" from nuclear energy.
A thousand people also gathered in the western German city of Perl to demand the closure of the nuclear power plant across the border in the French town of Cattenom some 16 kilometres (10 miles) away, charging that it is unsafe.