Mr Macron secured a second term as French president after he defeated far-right candidate Marine Le Pen.
Mr Morrison welcomed Mr Macron's election win on Twitter.
"Congratulations Emmanuel Macron on your re-election as president. A great expression of liberal democracy in action in uncertain times," he said.
"We wish you and France every success, in particular your leadership in Europe and as an important partner to Australia in the Indo-Pacific."
Labor deputy leader Richard Marles also congratulated Mr Macron following his election victory.
"France is our neighbour, France is a Pacific country, and as such, France matters deeply to Australia," he told reporters in Darwin.
"It is a profoundly important relationship in Australia's world view, and we certainly look forward to working with President Macron as he leads France over the coming years."
Diplomatic relations between the two nations have been tense in recent times, following Australia's decision to scrap a multi-billion dollar submarine contract with France in favour of nuclear-powered vessels with the AUKUS security pact.
At last year's G20 summit, Mr Macron accused Australia's prime minister of lying to him about the terms of the submarine deal.
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