Voters handed her CDU party and its centre-left coalition partner SPD their worst score in European election history, while doubling support for the Greens amid rising fears over global warming.
The Greens also snatched second spot from the Social Democratic Party, coming in just behind Merkel's centre-right alliance.
Crucially, the environmental party took more than a million votes -- including many from young people -- each from the SPD as well as from the CDU.
Der Spiegel said the coalition is "in danger" after Sunday's drubbing.
"This instability can lead to a break up at any time. The CDU and SPD are deeply insecure parties. If, for example, SPD leader (Andrea) Nahles were to fall, the question of the continued existence of the coalition would immediately arise."
The SPD, stung by a beating at general elections in 2017, had initially sought to go into opposition.
But it was reluctantly coaxed into renewing a partnership with Merkel's centre-right alliance, and many within the party remain wary of continuing to govern in her shadow while taking the fall for any unpopular policies.
With the SPD also losing the top spot in stronghold Bremen during state elections Sunday, rumblings of discontent against the leadership may yet grow louder.
Already ahead of the vote, Bild am Sonntag quoted unnamed sources as saying that veteran politician Martin Schulz was ready to stand against Nahles when the parliamentary chief post comes up for renewal in September.
Slapping down the speculation, finance minister Olaf Scholz warned against putting Nahles' role in question.
"Calling for personal consequences would not help," he said.
- Blindsided -
But the SPD was not the only party in crisis mode after Sunday's debacle.
Merkel's CDU too had been blindsided by youth-led anger over global warming.
Key party figures admitted Sunday that they had campaigned on the wrong topics, as they overlooked climate which had overtaken immigration to become the main worry for Germans this year.
The momentum for the Green surge had been building up over months as the strikes started last November by Swedish activist Greta Thunberg, 16, not only refused to lose steam but caught the imagination of youth across the world.
The Greens were further lent a boost in Germany by a prominent YouTuber whose online assault against Merkel's coalition accusing it of failing to act to halt global warming went viral.
The CDU struggled for days to put out the fire.
Just two days before the vote, the online star Rezo upped the ante and published a joint call with 70 influential YouTubers telling their millions of followers to shun parties in Merkel's coalition as well as the far-right AfD at the polls.
On Sunday, one in three under-30s picked the Greens, while only 13 percent picked the CDU. The SPD also did not fare better, winning over only 10 percent of the age group.
Party chief Annegret Kramp-Karrenbauer, who is poised to succeed Merkel when the veteran leader steps down in 2021, conceded: "Yes, we made mistakes in this election campaign, that has to be said."
Markus Soeder, who heads Merkel's Bavarian allies CSU, declared the environmental party its main rival.
"The biggest challenge of the future is the intensive debate with the Greens," he said, adding that "old measures that we had before, are no longer valid".
Underlining that the CDU-CSU bloc was struggling to win over young voters, he added that "we must work to be younger, cooler and more open".