"She praised him for championing a united European Union that is open to the world," said her spokesman Steffen Seibert.
"The decision of French voters is therefore a clear commitment to Europe," he said, adding that Merkel had telephoned Macron to congratulate him.
Earlier, Seibert had written in German and French on Twitter: "Congratulations, @EmmanuelMacron. Your victory is a victory for a strong and united Europe and for French-German friendship."
Separately, German Foreign Minister Sigmar Gabriel welcomed Macron's win for keeping France "at the heart of Europe".
"Liberte, Egalite, Fraternite! France chose that today. The great nation was, is, and remains in the middle and at the heart of Europe," wrote Gabriel on Twitter, using France's national slogan which means "liberty, equality, fraternity".
Merkel and her government had thrown their support behind Macron against far-right and anti-EU challenger Marine Le Pen.
Critics of the tough push for economic reforms have argued that such policies may have pushed some to the political extreme.
"What has to stop is pointing fingers at the French for doing nothing and not giving them a milimetre of flexibility in their policies,"he said.
"Maybe the conservatives in Germany now realise that 0.5 percent more deficit in France is really not as costly as if Madame Le Pen were president," he added.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)
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