The result will give the ecologist party high hopes for a much bigger prize: success in an election next Sunday in the wealthy southwestern state of Baden-Wuerttemberg, the most important of the year's electoral tests.
Projections in Saxony-Anhalt indicated Merkel's Christian Democrats (CDU) came first and were likely to stay in power in coalition with their sworn enemies at national level, the centre-left Social Democrats (SPD).
This was despite the CDU's share of the vote slipping some three percentage points to 32.7 per cent. The SPD's share of the vote was little changed on 21.5 per cent, behind the far-left Die Linke, on 23.8 per cent, also little changed.
But the big winners of the vote in the impoverished eastern state -- unemployment stands at 13 per cent -- were the Greens, who more than doubled their score to seven percent.
The far-right NPD won 4.5 per cent, below the five percent needed to enter the state parliament. The pro-business Free Democrats (FDP), Merkel's coalition partners at federal level, will also be unrepresented, scoring 3.5 percent.
The surge in the Greens' support was seen as being in large part down to Merkel's stance on nuclear power after Japan's earthquake and tsunami on March 11 pushed reactors at the Fukushima plant to the brink of a meltdown.
People "want to know, particularly after the tragedy in Japan, what a responsible energy policy will look like", Greens co-head Claudia Roth said.
The result, although driven to a large extent by local issues, "showed one thing: that the rise of the anti-nuclear movement is only boosting the Greens", the Stuttgarter Zeitung daily said in today editorial.
Baden-Wuerttemberg, where the CDU have ruled since 1953 -- the year before Merkel was born, is home to four nuclear reactors. Saxony-Anhalt has none, but has several wind farms.
Germany decided a decade ago to go nuclear-free by around 2020 but Merkel last year postponed the switch-off until the mid-2030s despite strong public unease about atomic energy.
But Japan's nuclear emergency prompted her last week to announce a three-month moratorium on the postponement and the temporary shutdown of Germany's seven oldest reactors pending a safety review.