As police fired tear gas and stun grenades to halt angry crowds chanting anti-austerity slogans and waving swastika flags, Mrs Merkel's host, Prime Minister Antonis Samaras, welcomed her as a friend.
Blamed by many Greeks for imposing draconian budget cuts in exchange for aid, Mrs Merkel reaffirmed Berlin's commitment to keep the debt-crippled Greek state inside Europe's single currency.
"I have come here today in full knowledge that the period Greece is living through right now is an extremely difficult one for the Greeks and many people are suffering," Mrs Merkel said during a joint news conference with Mr Samaras just a few hundred yards from the mayhem in Syntagma Square, outside Parliament.
"Precisely for that reason, I want to say that much of the path is already behind us," she added, offering a public display of support to Mr Samaras's three-month-old Government on her first visit to Greece since 2007.
She tried to reassure her hosts their reforms would eventually pay off, but also made clear that Greece, which has seen its unemployment rate surge to nearly 25% and economic output shrink by one-fifth, would not solve its problems overnight.
Mr Samaras promised to implement economic reforms necessary to restore confidence. "The Greek people are bleeding but are determined to stay in the euro," he said.
On the other side of the parliament building, tens of thousands of demonstrators defied a ban and gathered to voice their displeasure with the German leader. Many blame her for forcing painful cuts on Greece in exchange for two European Union-International Monetary Fund bailout packages worth more than €200 billion (£161 billion).
Police fired teargas and stun grenades when protesters tried to break through a barrier to reach the cordoned-off area where Mrs Merkel and Mr Samaras were meeting. Some demonstrators pelted police with rocks, bottles and sticks.
Four people dressed in Second World War-era German military uniforms and riding on a small jeep, waved swastika flags and made Nazi salutes.
Banners read "Merkel out, Greece is not your colony" and "This is not a European Union, it's slavery". Some 6000 police officers were deployed, including anti-terrorist units and rooftop snipers, to provide security during the six-hour visit. German sites in the Greek capital, including the embassy and Goethe Institute, were under special protection.
After steering clear of Greece, Mrs Merkel is now keen to show support for Mr Samaras, a fellow conservative, as he struggles to impose more cuts on a society fraying at the edges after five years of recession.
With a year to go until Germany holds a parliamentary election, Mrs Merkel is also hoping to neutralise criticism at home that she has neglected Greece and contributed to its woes by insisting on crushing budget cuts.
After her Government flirted earlier this year with the idea of allowing Greece to exit the eurozone, she now appears determined to keep it in – at least until the German election is out of the way.
Greece is in talks with its "troika" of lenders – the EU, European Central Bank and IMF – on the next tranche of a €130bn loan package, its second bailout since 2010.
Without the €31.5bn tranche, Greece says it will run out of money by the end of November.
Mrs Merkel said the aid payment was urgently needed but stopped short of promising that the funds would flow.
Mrs Merkel said: "The troika report will come when it is ready. Being thorough is more important than being quick.
"We are working hard on this, but we must resolve all the problems.I think we'll see light at the end of the tunnel."
Ties run deep between Greece and Germany, where more than 300,000 Greeks currently reside.
But the relationship is clouded by atrocities Greeks suffered at the hands of the Nazis. Mr Samaras's own great-grandmother killed herself after she watched Nazi tanks rolling down the streets of Athens and the swastika flying over the Acropolis.
l French riot police used teargas to disperse protesters outside the Paris auto show yesterday, during nationwide demonstrations over mounting job losses and unemployment, which is at its highest since 1999.