The incident came during the decider as the chair umpire overruled the line-umpire's decision on a line-call and awarded a point to Jorgensen when Prannoy was leading 13-11.
By the time Prannoy realised what had happened, he had run out of time to challenge the decision.
"Though I lost the point, I was determined to keep my focus on the game," he said after the match. "I have had some pretty close calls in many tournaments, so I did not let the coach's and crowd's agitation get to me.
"The conditions were suitable for me and I was playing really fast as I knew Jorgensen doesn't like my style of playing. Overall, it was a really good game and the incident did not bother me."
Despite the incident, the 22-year-old could not hide his jubilation after beating Jorgensen in a hard-fought contest.
Prannoy was forced to toil and dig deep for his victory as the Dane pushed him to his limits. But, despite losing the first game, Prannoy refused to be deterred as he rallied back to stun Jorgensen 18-21, 21-14, 21-14 in just under an hour.