When a popular state governor was shunted aside this week, it might have been just another local political wrangle. But not in Germany, at the current moment, with the far right resurgent.

The maneuvering found Chancellor Angela Merkel’s conservatives voting with the rival Alternative for Germany, raising alarms that they had violated a taboo among mainstream parties against working with the far right. The reaction was fast and furious.

“A pact with fascism,” one headline screamed. Another gasped about “a coup.” Protesters gathered spontaneously in major cities across the country, chanting anti-fascist slogans. Even the chancellor weighed in from afar during a visit to South Africa: “It was a bad day for democracy,” she said darkly.

Three years after the Alternative for Germany became the first far-right party to enter Germany’s national parliament since World War II, the events underscored how the country’s beleaguered traditional parties are still struggling to deal with the new disruptive force.

Nevermind that on Friday, just more than 48 hours after the mini-coup in the tiny eastern state of Thuringia, the right’s favored candidate looked certain to step down in the face of the popular backlash. The parties will now have to find a compromise candidate or hold new elections.

The small drama had already succeeded in setting off a big round of soul-searching in Germany, which is still deeply conscious of its Nazi past and anxious about where the present inroads by the far right might lead.

For many Germans, allowing the far right to be kingmakers conjures up dark memories. It is a red line that many do not want to see crossed.

“Just looking at the reaction you could be forgiven for thinking that the Third Reich has been resurrected,” said Jan Techau, director of the Europe Program at the German Marshall Fund in Berlin.

“Deep down we Germans don’t trust ourselves,” Mr. Techau added. “That is one legacy of the Hitler era.”

It did not help that Thuringia is precisely where, in the dying days of the Weimar Republic more than 90 years ago, the Nazis first won power locally, before going on to win nationally — with the help of conservative parties.

This history echoed loudly across the country.

“A whiff of Weimar — I say, not exaggerating and having reflected deeply on this — hangs over the republic,” Gerhart Rudolf Baum, a former center-right interior minister, told German public radio.

The taboo of not collaborating with the AfD, while sacred, is at risk of crumbling in an increasingly fragmented political landscape.

So far, no German state governor has been elected with support from the Alternative for Germany.

But the Alternative for Germany has steadily broadened its presence in state legislatures. Especially in eastern states, it has in recent elections been among the top finishers.

That is what happened in Thuringia in state elections last October, when the AfD doubled to its share to 23.5 percent and finished second, ahead of Ms. Merkel’s conservatives.

The winners, though short of a majority, were a coalition of progressive and left-wing parties. So, this week, when the leftist incumbent asked the state legislature to approve his coalition as a minority government, everyone expected him to win.

Instead, the AfD surprised everyone when it threw its support behind a little-known candidate of the center-right Free Democrats, who had only five representatives in a state house of 90.

He also had the backing of the local chapter of Ms. Merkel’s conservatives, giving him enough to win.

The move by the AfD amounted to a political ambush. But it also prompted thinly veiled accusations of collaboration.

“The means do not justify the ends and power does not trump decency,” wrote Sigmar Gabriel, a Social Democratic former foreign minister. That was a lesson that “should have deeply and indelibly enshrined’’ in the memory of mainstream parties, he added.

Bodo Ramelow, the leftist governor, who got beaten in Wednesday’s vote, reacted swiftly by tweeting a quote from Hitler in 1930, the year his Nazi party gained its first foothold in Thuringia.

“We achieved the biggest success in Thuringia,” Hitler had boasted at the time. “There we are today really the decisive party. The parties in Thuringia that have governed so far, are unable to get a majority without our assistance.”

The events in Thuringia were all the more symbolic — and significant — because it is the fief of the AfD’s most notorious far-right leader, Björn Höcke. A history teacher turned far-right ideologue, Mr. Höcke uses language that is packed with echoes from the 1930s and has called the Holocaust memorial in Berlin a “memorial of shame.”

He also runs a movement inside the AfD known as the Flügel, or Wing, which is under observation by the intelligence service on suspicion of extremism.

A court last year ruled that it was in fact legitimate to call him a “fascist.”

The photo of Mr. Höcke shaking hands with the victorious center-right candidate, Thomas Kemmerich, prompted particular outrage.

“Handshake of shame” the front page headline of the tabloid Bild read. The new governor “gets elected by neo-Nazi Höcke.”

But even beyond Thuringia, enforcing a ban on cooperating with the AfD is proving to be tricky. In small towns, the local face of the AfD may be the doctor or firefighter. Political ideology feels less of an obstacle when the issues of the day are things like road repair or renovating the nursery school.

A report last year by ARD, Germany’s public broadcaster, identified at least 18 cases of cooperation between the AfD and mainstream parties.

In the northern town of Eilsleben, the Christian Democrats invited an AfD representative into their group. In Görlitz, near the Polish border, an AfD candidate was elected to a local committee after receiving support from mainstream parties in the town council.

In the small western town of Frankenstein, a short-lived coalition was even agreed between a Christian Democrat and an AfD member who were husband and a wife.

But Thuringia took the dynamic from the local municipal level to the state level. Some fear it is only a question of time before it arrives on the federal level, where the AfD is the leading opposition party in the national parliament.

Even inside the conservative camp, some voices are urging the rethinking of the policy of the cordon sanitaire around the AfD.

Martin Patzelt, a vocal defender of Ms. Merkel’s 2015 refugee policy and member of her conservatives, is no friend of the AfD. But he said he understands why isolating the party riles its voters — and some conservative Christian Democrat voters, too.

“We can’t stick our heads in the sand and pretend they’re not there,” Mr. Patzelt said in a recent interview before events unfolded in Thuringia. “The AfD is not going away. We need to learn how to deal with them in a mature way.”

The AfD, meanwhile, has enjoyed accusing mainstream parties of distorting democracy by ignoring the will of voters. For it, the week’s events served as a case in point.

“The AfD can’t be bypassed anymore,” Alice Weidel, leader of the AfD’s parliamentary group, said triumphantly.