The protesters appeared to be targeting riders from the Israel Premier-Tech team on Wednesday.
Some attempted to invade the road when the riders of the Israeli team crossed in front of them, prompting organisers and security staff to rush in to try to contain them behind the security fences.
Police were called in to contain the protesters, many of whom carried Palestine flags and pro-Palestine signs.
Race officials made an announcement to the teams as the riders had about 10km to go in the 157.4km stage that also started in Bilbao.
"Due to some incidents at the finish line, we have decided to take the time at three kilometres before the line. We won't have a stage winner. We will give the points for the mountain classification and the intermediate sprint, but not on the finish line," they said.
The start of the stage also had been disrupted by protesters who forced race officials to pause the peloton for a few minutes.
The police appeared to have the crowd under control by the finish, forming a line to keep the protesters from going over the security fences, but officials decided it was safer to keep riders from reaching that point.
Race leader Jonas Vingegaard said it was disappointing not to be able to finish the stage.
"It's a big shame, we really would have loved to win the stage," he said, adding that he was looking forward to a strong finish by his team on the day of his son's birthday.
Britain's Tom Pidcock had been ahead with Vingegaard and there was a surreal end to the race, with the pair unsure of where exactly the new finish line was.
"It's hard to describe the disappointment, to be honest," said Pidcock, who had ridden a spectacular race.
"I felt like today was my day. I feel like there should always be a finish line."
The Briton also had a message for the protesters.
"Putting us in danger isn't going to help your cause," he said.during the final parts of the stage.
