It's not entirely clear what De Jong's injury is. He didn't have any kind of high-impact incident, wasn't noticeably limping and wasn't reported to be dealing with an injury coming into the match. He exited under his own power.
The change is an odd one because Martins Indi was thought to be left out of the starting XI due to an injury. He was playing well for the Netherlands before sustaining a head injury in their second game. Because the starting lineup featured Daley Blind out of position at left central defense and Dirk Kuyt out of position at left wingback, most assumed that Martins Indi was not fit enough to play.
There's no truly natural replacement for De Jong in the Netherlands team. With this substitution, Martins Indi will take over Blind's position in defense and Blind will move into De Jong's defensive midfield role.