Earlier on Friday, Mr Obama and Ms Merkel vowed to "redouble" efforts to achieve peace in the Middle East in talks in Dresden.
One day after making a keynote speech in Cairo, Mr Obama said his government would seek a resumption of peace talks between Israel and the Palestinians.
"The moment is now, to act on what both sides know to be truth," he said.
Mr Obama and Mrs Merkel each carried a long-stemmed white rose as they toured Buchenwald with Holocaust survivor and Nobel prize winner Elie Wiesel.
They laid the roses at a memorial plaque for the more than 56,000 people who died at the camp, before taking a tour of the barracks and crematorium.
He described the camp as the "ultimate rebuke" to people who would deny the Holocaust.
Earlier, Mr Obama suggested Iranian President Mahmoud Ahmadinejad - who this week repeated his claims that the Holocaust was a "great deception" - should make his own visit to Buchenwald.
"I have no patience for people who would deny history," he said in an interview in Germany with NBC News," and the history of the Holocaust is not something speculative."
He made similar comments in his speech in Cairo, in which he called for a "new beginning" in US relations with the Muslim world.
Mr Obama was vague on Friday about the exact steps his administration would take to achieve this, but said he would send his special envoy George Mitchell back to the region to meet leaders and discuss the issues raised by his Cairo speech.
Mrs Merkel said she and the US president had discussed a timeframe for diplomatic action in the Middle East and pledged to offer whatever help Germany could provide.
At a joint news conference, the two leaders talked about the other issues they had discussed:
• On Iran, Germany pledged to work with its contacts and use its "expert knowledge" as one of the key European negotiators with Tehran. Mr Obama said the US viewed the Iran issue in the "broader context" of preventing a nuclear arms race in the Middle East
• Mr Obama praised Germany as a "strong Nato partner" and spoke of the challenges ahead in Afghanistan, but stopped short of explicitly calling for more European troops
• The German chancellor gave no firm commitments on German assistance with terror suspects currently held at Guantanamo Bay, Mr Obama said, but said Europe would work with him as he seeks to close the prison camp
• Both leaders pledged to continue along the path of financial regulation set out at April's G20 summit
• On climate change, Mrs Merkel said the world faced an "uphill challenge", adding that both the US and Germany would seek a workable deal at a major climate conference in Copenhagen later this year
Other elements of Mr Obama's visit to Germany are more nuanced.
Mr Obama needs to convince an increasingly sceptical American public that the war in Afghanistan is worth fighting, the BBC's Steve Rosenberg in Berlin says.
So he will use his trip to Germany - and then the D-Day commemorations in France - to send a strong message back home that the fight against tyranny demands sacrifice, our correspondent says.
He will be hoping that Europeans, too, get the symbolism of his visits to Buchenwald and to Dresden, a city locked behind the iron curtain until the defeat of communism.
Mr Obama wants European governments to shoulder more of the burden in Afghanistan, to send more combat troops to take on the Taliban.
He also wants European countries to take in dozens of detainees from Guantanamo Bay, but like Germany, there has been little enthusiasm so far.
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