He charged that Merz's tactic of accepting votes from the Alternative for Germany late last month had meant "a breaking of his word and of a taboo".
"And therefore one cannot be sure what the future will be like when things become difficult again," he added.
Post-war Germany had done "very well in the past decades when the democratic parties agreed not to cooperate with the extreme right", said Scholz.
He also charged that Merz's plans to push back undocumented migrants at the border would risk "a European crisis" and asked "how could one be so stupid?"
No co-operation with AfD
Merz stressed that his Christian Democratic Union (CDU) and their Bavarian allies the CSU, if they win the election, would not cooperate or rule with the anti-immigration AfD.
"I want to make it clear here once again that we will not do that," Merz said, adding that "there is no common ground" between his CDU and the AfD.
Merz said he had been driven to act after a crime that shocked Germany, a knife attack on a kindergarten group that killed a two-year-old boy and a man trying to help the toddlers.
"I could no longer justify it with my conscience," said Merz of the option of waiting any longer before launching a motion on his promised crackdown on irregular immigration.
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Scholz listed progress made by his coalition government at the national and EU level to control irregular migration, but Merz accused him of "living in a different world" to German citizens.
The knife rampage, where police arrested an Afghan suspect, was the latest in a series of deadly attacks that have darkened the mood in Germany over the arrival of millions of war refugees and other asylum seekers in recent years.
But tens of thousands have also taken to the streets of Germany to protest against the conservatives' breach of the long-standing "firewall" against the AfD.
Germany 'deindustrialising'
Merz, whose party is polling at around 30 percent, is banking on going "all in" on immigration to peel away voters tempted by the AfD, which is polling in second place with at least 20 percent of the vote.
The Social Democrats of Scholz and the Greens are both trailing at around 15 percent.
The rivals also clashed on the ailing economy. While Scholz advocated investment to help struggling businesses and a higher minimum wage Merz blamed his government for Germany now "deindustrialising".
"We are now in the third year of a recession," Merz said. "That has never happened in Germany before. We have three million unemployed in Germany and the trend is rising."
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Scholz pointed to high energy costs sparked by Russia's full-scale invasion of Ukraine. "I did not invade Ukraine," he said.
The two candidates mostly agreed on major foreign policy goals and the need to raise defence spending, but differed somewhat on how Berlin should deal with US President Donald Trump.
Scholz labelled Trump's plan to take control of Gaza and empty the war-ravaged Palestinian territory "a scandal", adding that "the relocation of a population is unacceptable and against international law".
"I share this assessment," said Merz, while adding that "we have to wait and see what is really meant seriously and how it will be implemented. There is probably a lot of rhetoric involved."
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Like many other observers, ING bank analyst Carsten Brzeski judged that the relatively "well-behaved" 90-minute debate ended with a draw.
The debate "is unlikely to significantly have moved the needle in the election campaign," he wrote.
"Tone and content leave the door open for another grand coalition after the elections, even though coalition talks are likely to be complicated."
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