The incident occurred as Raisner was trying to assist German modern pentathlete Annika Schleu on Friday, ahead of her show jumping round in the women's event.
Schleu was seen visibly struggling to control Saint Boy, the horse she had been assigned to jump with.
"The UIPM Executive Board has given a black card to the Germany team coach Kim Raisner, disqualifying her from the remainder of the Tokyo 2020 Olympic Games," the UIPM said.
"The EB reviewed video footage that showed Ms Raisner appearing to strike the horse Saint Boy, ridden by Annika Schleu (GER), with her fist during the Riding discipline of the Women's Modern Pentathlon competition."
Saint Boy was bucking and refusing to trot around the ring as Schleu tried to rein him in.
Athletes in the pentathlon are assigned horses to compete on at random and are given only 20 minutes to bond with their horse before the show jumping round begins.
"Today's competition in riding in the modern pentathlon was partially characterized by scenes that damaged the image of the sport," said the German Olympic Committee in a statement sent to CNN on Saturday.
"Numerous recognizable excessive demands on the horse, and rider combinations should be an urgent reason for the international association to amend the rules.
What's next for Simone Biles after Tokyo Olympics?
"It needs to be changed so that the horse and the rider are protected. The welfare of the animal and fair competition for the athletes needs to be the focus."
The UIPM did not immediately respond to CNN's request for comment on the assignment of horses in the competition and the issue of animal welfare.
CNN has also reached out for comment from Raisner and Schleu via the German Olympic Committee.
"I said 'hit it.' However in no way did she harm the horse," Raisner was quoted as telling Germany's Sport Information Service, according to DW and other German media outlets.
"The fact that you hit the back with your whip is no longer considered torturous. It didn't tear the horse's mouth, it didn't have any sharp spurs on it, torturing horses looks different."
'I just started crying'
Schleu, who had been leading the field ahead of the show jumping event, was in tears as she came into the ring riding Saint Boy.
Raisner could be heard on TV telling Schleu to hit the horse to get Saint Boy to behave.
Raisner was then seen hitting the horse once above his back leg. The incident was quickly picked up on social media, sparking a debate about the welfare of horses taking part in the modern pentathlon.
After the show jumping round Schleu said she felt Saint Boy lacked confidence.
"I talked to the (owner of her horse) and she said just gallop in and let him go," Schleu told reporters on Friday. "I tried but he did not want to go. I just started crying."
"I did not expect to make him go and that was the reason I was crying."