Bokeloh was a key animator during the final lap but still found the energy to take the bunch sprint, beating Russian Alexandr Kulikovskiy and Dutchman Peter Lenderink to the top of the podium.
Jai Hindley was the best of the Australians in 24th on bunch time, with junior time trial world champion Michael Storer 27th, and James Thompson 34th.
"I'm pretty happy. Would have be nice to stand on the podium but we gave it all we had," said Hindley. "None of us are really sprinters so our plan was to go hard over the last climb."
A blistering pace was set from the start of the 127km race, discouraging attackers from trying to breakaway too early. American Adrien Costa was the first to make a meaningful skirmish as he soloed off the front with four laps of the seven to go.
The peloton was all together at the beginning of the final lap.
A dangerous six man group formed, including Columbian rider Wilmar Paredes, who tried his luck a couple of times, but they were soon passed by a trio from Italy, Russia and Kazakhstan, with eventual victor Bokeloh also bridging across.
Yet another small group forged clear over the final climb up to Mirador, with Swiss youngster Gino Maeder flying down the descent into town in the lead.
Maeder and Russian rider Stepan Kurianov had a narrow advantage turning onto the final straight, but the four-strong Belgian team dragged them back with 300m to go, leaving the Rainbow Jersey to be decided by a sprint.
Bokeloh powered away with 200m to go to win by half a bike length.
Junior Men: 127.4km, Ponferrada
1 Jonas Bokeloh (GER) 3hr 7min
2 Alexandr Kulikovskiy (RUS)
3 Peter Lenderink (NED)
4 Edoardo Affini (ITA)
5 Magnus Klaris (DEN)
6 Izidor Penko (SLO)
7 Lucas Eriksson (SWE)
8 Lorenzo Fortunato (ITA)
9 LÃ©o Danes (FRA)