Earlier, Van Marwijk and retiring captain Giovanni van Bronckhorst, who played his last game of professional football in Sunday's finale, were knighted by Prime Minister Balkenende at his official Catshuis residence.
Balkenende, sporting an orange tie, served the squad coffee and cakes with orange icing in his garden, which was decorated with orange balloons. "The Netherlands is proud of Oranje," he said.
The players then went by by coach to meet Queen Beatrix at her Noordeinde Palace in The Hague, before being taken by helicopter to Amsterdam.
After completing their boat trip, the squad was introduced, one by one, to hundreds of thousands of fans gathered at Amsterdam's Museum Square. City police tweeted that, all told, an estimated half a million people had come along to cheer their heroes.
The parade was originally scheduled to take place only if the Netherlands had returned home as champions, but Amsterdam officials released a statement saying: "Even in second place, the Dutch team are champions in the eyes of their country."
By contrast, Germany - beaten by Spain in the semi-finals - made a low-key return from South Africa after turning down the chance of a welcome home party.
After landing in Frankfurt the players went their separate ways and did not speak to fans who had gathered at the airport, prompting complaints from some.
An open letter published on the national team's official website said they "deeply regretted" the "displeasure and incomprehension" caused and didn't intend to upset anyone. The letter added that they didn't want to celebrate finishing third as "this team wants more, for itself and its fans."
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