Macron said in a joint news conference he would be an "open, direct and constructive partner" of Germany and also called for more "pragmatism" in bilateral relations.
Berlin hopes to gain new momentum and support from Paris for reforms of the European Union in general, but particularly for the eurozone. While Merkel and Macron did not decide on any specific measures, they agreed to stick to a "road map" of talks and negotiations.
"We can give the entire [European] construct a new dynamic," Merkel said, adding that Europe could progress only with a "strong France" within.
Germany and France are the eurozone's two biggest economies. It is a long-standing tradition that French presidents choose the German capital for their first official visit.
During his campaign, Macron presented ideas on reforming the eurozone, noting the currency bloc cannot go on as it is if it wants to avoid falling prey to protest and populism. Among reforms he wants to see are setting up a separate budget for the 28-member group, as well as giving it its own parliament and finance minister.
But the proposals sent alarm bells ringing in Berlin, and initial relief about his victory against far-right leader Marine Le Pen had quickly given way to fears about his reform plans.
German Finance Minister Wolfgang Schaeuble warned such deep-reaching reforms would require treaty changes, which were "not realistic" at a time when Europe is being hit by a surge of anti-euro populism.
But at the press conference following their talks, Merkel adopted a conciliatory tone and offered what appeared to be a key concession.
"From the German point of view, it's possible to change the treaty if it makes sense," she said.
Macron said France and Germany had come "at a historic moment in their history" and both have a responsibility to fight against populism and restore faith in the European project.
He also announced he would initiate "deep reforms" in France in order to tackle unemployment.