The 22-year-old Frenchman, who won the Goal of the Tournament award at the 2018 World Cup, was left with brutal stud marks on his neck.
Pavard was making a sliding tackle on Rudiger on the wing when the incident took place.
Rudiger's studs seemed to scrape across Pavard's neck, although no free-kick was awarded for the stamp.
Rudiger appeared unaware of what he had done, walking away without a look back as Germany prepared to take a corner.
Despite the incident, which took place after just 3 minutes of play, Pavard battled through to play the full 90 minutes.