Van Persie's irate reaction at being substituted in the 2-1 win over Slovakia threatened to derail preparations for the quarterfinal against Brazil.
Van Marwijk said Tuesday he called a team meeting after reports in Dutch media that the striker said midfielder Wesley Sneijder should have been brought off instead of him.
"I will never accept anything that could upset the next match," Van Marwijk told Dutch national broadcaster NOS.
"I spoke to Robin and he is supposed to have said something about Wesley. I've spoken to Wesley and after that I called the team together ... told them what I think and then drew a line under it."
He did not elaborate, but his swift action was clearly intended to preserve unity in the buildup to Friday's quarterfinal in Port Elizabeth.
Previous Dutch campaigns have been rocked by infighting, but the team had appeared unified in South Africa.
Van Marwijk insists he nipped the latest dispute in the bud.
"I've always said I don't mind if something happens - that can make you stronger - but I don't like to leave problems dangling," he said. "It's over. For everybody."
Van Persie and Sneijder did not speak to the media Tuesday, but Van Persie denied Monday having said Sneijder should have been replaced instead of him.
Van Marwijk said he did not hear what Van Persie said to him after the substitution because of the din of vuvuzelas in Durban's sold-out Moses Mabhida Stadium. Sneijder did not speak to reporters after the Slovakia match.
Van Persie and Sneijder have a history of tense relations dating back to a public spat over who should have taken a free kick in the 2008 European Championship quarterfinal loss to Russia.
Van Persie was clearly angry at being substituted Monday, believing chances were about to come his way.
"I wanted to finish the game. I thought they would take risks in the last 10 minutes and I wanted to exploit that," Van Persie said after the game. "I could see spaces opening up and I wanted to use them, so I was a bit shocked when I had to go off."
Immediately after the match, Van Marwijk played down any dispute with his starting striker, who has scored 19 goals in 48 internationals.
"I shook his hand and understood that he was disappointed; that's not a bad thing," Van Marwijk said Monday. "Everyone wants to play the whole game."
The most famous case of Dutch disunity was at the 1996 European Championship, when coach Guus Hiddink sent midfielder Edgar Davids home early for insulting him in an interview. That talented squad reportedly also was divided between black and white players.
Van Marwijk's predecessor, Marco van Basten, also fell out with Davids, Mark van Bommel and Clarence Seedorf and famously criticized Ruud van Nistelrooy during the 2006 World Cup.
They should get their shit together before facing Brazil or it's gonna be CARNAGE. Kiss and make up, release some of that unresolved sexual tension if you know what I mean.
Gif of the incident, courtesy of dreamfight3r: