In the new accord, meant as a follow-up to the 1963 Elysee Treaty, both France and Germany pledge to stand shoulder to shoulder in case of a military attack against either of them, reaffirming a commitment already written into European Union and NATO treaties.
The ceremony comes on the anniversary of a similar treaty in 1963, signed by Charles de Gaulle and Konrad Adenauer.
But the text, promising enhances security, economic and practical cooperation, was heavily criticised by domestic far-right opponents in France and Germany as signing away national sovereignty, and derided by eurosceptics overseas as a symbolic and irrelevant gesture by two significantly weakened leaders.
"In this context, confirming this belief in Franco-German cooperation has symbolic value", she told German public radio.
"Maybe the expectations for France and Germany continuing to shape Europe have become too high", Dempsey said.
Amid the headwinds, German magazine Spiegel Online noted that while the treaty "is full of good intentions, it lags far behind what is necessary".
But at home, Mr Macron's critics on both the far-left and far-right have seized on the treaty as an erosion of French sovereignty.
Called Aachen in German, Aix-la-Chapelle is the most westerly German city.
The new agreement aims to deepen French-German cooperation in education, the environment, security and economic policy, among other areas.
Eurosceptics were unimpressed by the new treaty. The two countries also want stronger cooperation on environmental and climate policies.
The French presidency said that "by trying to rekindle the ashes of a rivalry between France and Germany, those who spread the false news betray all the work of reconciliation that allows us to live in peace". The German chancellor is eyeing the exit, having ceded control of her Christian Democratic Union party to an ally, Annegret Kramp-Karrenbauer. The French president, meanwhile, has come under fierce domestic pressure in the form of the anti-establishment, grassroots gilets jaunes (yellow vests) protest movement and plummeting approval ratings.
"We're seeing an existential crisis in terms of European integration, with Brexit and the expected strengthening of nationalists at the next European elections", said Claire Demesmay, a political scientist at German research institute DGAP.
A protester wearing a yellow vest faces riot police during a demonstration of the "Yellow Vests" (Gilets Jaunes) against rising costs of living on the Champs Elysees avenue in Paris, Dec. 8, 2018.
What is even more critical to realise is that power centres that run national politics are not absolute.
Other false rumours circulating online include the claim that France aims to share its permanent seat on the United Nations security council with Germany, part of broader accusations that the centrist president - as the far-right leader Marine Le Pen alleged - is determined to "dismantle the power of our country".
In her weekly address Saturday, Merkel said she and Macron believe that "the world has changed dramatically and we want to draw on what Germany and France have already achieved together".
Though short on detail, the treaty extension, negotiated over the past year, stipulates that it will be a priority of German-French diplomacy for Germany to be accepted as a permanent member of the United Nations Security Council.
Brexit is proving a big headache for the leaders of the European Union.