The Mexican government said that Kushner was recognised for his "significant contributions" during negotiations on updating the North American Free Trade Agreement.
That process culminated here on Friday in the signing of a new pact, the US-Mexico-Canada Accord, by Trump, Peña Nieto and Canadian Prime Minister Justin Trudeau.
Peña Nieto pinned a badge to the lapel of Kushner's jacket and handed him the medal and a diploma as Trump watched in silence from the front row.
Kushner, who is an adviser to Trump, said he was "honoured by the recognition" and he praised the work of Peña Nieto, whose successor, Andres Manuel Lopez Obrador, will take office Saturday.
"You have always put Mexican interests first even when it wasn't popular," Kushner told Peña Nieto, while insisting that Trump has "genuine respect and care" for the people of Mexico.
"I do believe we have been able to put that in the right light," Kushner said, adding that Mexico and the US are at a "historic moment."
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