FDP leader Philipp Rösler called the result a "bitter defeat". "But it shows now is the time to fight, dear friends," he said to applause from party supporters in Berlin. "This is a wake-up call for all liberals in Germany."
The results point to a strong likelihood that Merkel will clinch a third term next Sunday.
But they raise the prospect of a nail-biter finish to see whether she can continue her centre-right government or will have to form a "grand coalition" with her traditional rivals, the Social Democrats.
"The triumph of Christian Democrats' Bavarian sister party (CSU) belies the sizeable risks for them at the national level," news website Spiegel Online wrote, saying that a grand coalition now looked more likely.
"The good poll results in recent weeks and now the excellent CSU result could lead many CDU voters to think it's all over (and stay home on election day). Of even more concern to the Christian Democrats is the weakness of their coalition partner."
The conservative ruling Christian Social Union captured an absolute majority of seats in the Bavarian parliament with 49 percent of the vote, according to estimates on public television.
Its outsized victory means it can drop the FDP and govern alone.
"One Bavarian in two voted for us," incumbent state premier Horst Seehöfer told cheering supporters. "That is a huge vote of confidence."
Merkel campaigned hard in the state's world-famous beer tents, pointing out that a big win in Bavaria would lend momentum to her bid for another term at the helm of Europe's top economic power.
National polls give Merkel's conservatives an around 14-point lead over the main opposition Social Democrats (SPD), who scored about 21 percent in Bavaria, historically a conservative state.
However Merkel's chief election rival, Peer Steinbrück of the SPD, took heart from the Free Democrats' catastrophe.
"This is the 13th state election in a row in which the centre-right love match failed to win," he told public television. "There is a good chance that this will also happen on the federal level in a week's time."
The ecologist Greens turned in a dismal 8.5 percent, in keeping with a downward trend on the national level.
The CSU has ruled Bavaria uninterrupted for 56 years with a winning strategy of "laptops and lederhosen" – high-tech business savvy coupled with proud tradition.
The CSU saw big gains from its 43 percent score at the last election in 2008, when it lost its absolute majority.
Some 9.5 million were eligible to vote in the wealthy, predominantly Catholic southern region that is home to industrial giants such as BMW, Audi and Siemens.
Pollsters said the poor showing in Bavaria by the Free Democrats could in fact give them a boost in the September 22nd general election.
Voters who would like to see the Merkel alliance continue and who are concerned about the FDP's poor showing in Bavaria might now want to give votes to the party, dragging on the conservatives' own score.
That prospect led many Christian Democrats to warn any "pity" campaign for the FDP.
"The FDP will be fine on its own – stay cool, don't give away our votes," federal environment minister Peter Altmaier wrote on Twitter.
Merkel led a left-right grand coalition during her first four-year term. At the last election in 2009, a thumping 14.6-percent result for the Free Democrats allowed Merkel to form a government with the conservatives' traditional allies.