The World Cup runners-up face a Euro 2012 qualifying match against Moldova on Friday without the combative Manchester City player, who broke the leg of Newcastle United's Hatem Ben Arfa in a Premier League match on Sunday.
"This time Nigel crossed a line," Van Marwijk told reporters on Wednesday. "That is a shame as this matter only has losers.
"Ben Arfa broke his leg but Nigel lost as well and I can't use a player in great form during two important matches. But it didn't take me long to take this decision."
De Jong was involved in several controversial incidents last season, including a very high tackle on Spain's Xabi Alonso during this year's World Cup final.
"I spoke with Nigel on Monday and he was disappointed but I also had the idea he had some understanding for my decision," Van Marwijk added.
"I discussed with him in the past about the fouls he made but so far he never crossed the line like he did now."
Demy de Zeeuw and Theo Janssen were the most likely replacements for De Jong but the former has lost his starting position at Ajax and Janssen is injured.
In-form Tottenham Hotspur midfielder Rafael van der Vaart could step in. Winger Eljero Elia left the training camp with a heel injury on Wednesday, further reducing Van Marwijk's options as he also has to cope without injured forwards Robin van Persie and Arjen Robben.
The Dutch won their opening two games against San Marino and Finland and host Sweden next week after Friday's match in Moldova.
