"We have a big protest at three km before the line. We will decide the stage winner and take times at eight kilometres before the line," the race directors announced on Radio Vuelta.
The race had entered the final 15 km, with Bernal and Spain's Mikel Landa (Soudal Quick-Step) out in front, and the Colombian won the sprint to the new finish line, with Brieuc Rolland (Groupama-FDJ) coming in third.
A large group of protesters, waving Palestinian flags, had completely blocked the road on the ascent to the line, and the finish was moved to the foot of the climb, on the 167.9 km ride from Poio to Mos.Castro de Herville.
Landa and Bernal were part of a 17-man breakaway group early in the stage, and the pair had dropped everyone else by the time the announcement came, and Bernal, a former Tour de France and Giro d'Italia winner, claimed his first Vuelta stage win.
The peloton had been content to allow the riders up ahead to stay away, but on the penultimate climb the main bunch began to split, with the general classification contenders forming their own group.
Vingegaard, who suffered a puncture and needed to take one of his teammates bicycles, came in 15th, almost six minutes behind the stage winner, with the Dane's GC rivals alongside him.
The pre-race favourite remains 48 seconds ahead of Portugal's Joao Almeida (UAE Team Emirates XRG) with Britain's Tom Pidcock (Q36.5 Pro Cycling Team) third overall, over two and a half minutes down on the red jersey.
Previously there was no winner on stage 11, after organisers ordered the race to finish 3km from the line due to pro-Palestinian protesters causing disruption at the finish in Bilbao.
There were incidents on stage 10 which caused a rider to crash and also during stage five's team time trial when the Israel-Premier Tech team were stopped on the road by a group of protesters holding Palestinian flags.
Israel-Premier Tech removed their name from riders' jerseys on Saturday, but the protests have continued, with Javier Romo (Movistar) suffering a crash on Sunday's stage 15.
The Spanish rider was not at the start of Tuesday's stage, abandoning the race due to injuries picked up in the crash after a man with a Palestinian flag tried to run up to the riders and a policeman ran across the road towards the spectator.