Plapp produced a 52.443 km/hr ride over the 30.3 km course, besting the previous fastest speed in a world championships, set by fellow Aussie Damien Howson back in 2013 and his average speed of 52.380 over the 43.49 route.
He powered through the flat course, around the picturesque canals of the Flanders region in overcast conditions to the finish in Bruges.
The Australian wasn't the fastest in the early stages, but put in an impressive finish to bring it home strong in the finale, obliterating the provisional fastest time of Magnus Sheffield (USA) who will also join Plapp in 2022 as a neo-professional on INEOS Grenadiers.
He then had a nervous wait on the hotseat for the rest of the riders to come in, with the Australian eventually beaten by Pejtersen, the last rider to start. The Danish rider finished 10 seconds faster than Plapp, relegating the Australian into second and continuing a formidable run of success for Denmark in the Under 23 men's time trial, their fifth in six editions.
Plapp's performance was all the more remarkable with the Victorian 20-year-old having to recover from a crash at the Tour de l'Avenir that saw him fracture his elbow.
He was off the road for the next three weeks, but plowed his efforts into training at home and was back out in the real world with just over a week to go before the world championships. He had that time to get accustomed to his new time trial bike and finalise his physical condition for his first attempt at winning the Under 23 men's world championships.
Fellow Australian Carter Turnbull put in a strong ride to finish 15th overall, a minute and 15 seconds behind Price Pejtersen.
Plapp will not race the Under 23 men's road race, his next races will be the late season Italian classics as a stagiaire with INEOS Grenadiers.