Di Maio had already sparked annoyance in January when he accused France of leading colonial-style policies in Africa, prompting the French Foreign Ministry to summon the Italian ambassador.
The rupture, the first withdrawal of a French envoy to Rome since World War Two, was announced by the foreign ministry.
Italy's two deputy prime ministers, Matteo Salvini of the far-right League and Luigi Di Maio of the populist, anti-establishment Five Star Movement, have criticised the centrist French president, Emmanuel Macron, on a host of inflammatory issues, from immigration to the gilets jaunes (yellow vest) anti-government demonstrations in France.
Di Maio and Salvini, who formed a populist coalition government together previous year, have repeatedly criticised French President Emmanuel Macron, who has, in turn, targeted their "eurosceptic actions" before high-stakes European Parliament elections in May.
Di Maio's meeting with yellow vest activists came after Salvini called Macron "a awful president" in January.
And the Italian government last autumn accused France of dumping underage migrants over the border without authorisation.
Italy has accused France of helping to cause the migrant crisis.
He said the aim was to prepare a common front for European Parliament elections in May, while boasting on Twitter that "the wind of change has crossed the Alps".
"This new provocation is unacceptable between neighbouring countries and partners at the heart of the European Union", a ministry spokesman said in a statement a day after Mr Di Maio met the protesters on French soil.
De Maio's fellow Deputy Prime Minister Matteo Salvini, has also lambasted Macron directly.
"I hope the French will be able to free themselves of a awful president", Salvini said in a Facebook video last month.
The Yellow Vests are a thorn in his side and a controversy around his former bodyguard has resurfaced, threatening to arrest a pickup in his approval ratings. From his point of view, he said he has every right to begin a conversation with like-minded people: "I claim the right to be able to dialogue with all the European political forces - we want to create a group in Europe which is neither of the right nor of the left".
"We are ready and willing, with a constructive spirit, to turn the page for the good of our people", Salvini said.