Riders have crashed as a result of the protests, with some saying they have been worried for their safety.
Last week, Israel-Premier Tech began racing in modified jerseys which did not display their team name.
Organisers said: “It is still unknown whether there will be a winning ceremony with the situation as it is, with thousands of protesters filling downtown Madrid.
“The race has been officially ended and Jonas Vingegaard is the winner.”
Clashes continued after the race was abandoned, with protesters throwing bottles of water and other objects at police.
Race organisers had already shortened the 21st and final stage of the Vuelta from 111.6km to 103.6km.
Organisers did not specify a reason for the section removed, which would have crossed the plush Madrid neighbourhood of Aravaca.
Cycling journalist Brian Smith told BBC Sport: “They realised [there could be disruption] a few days ago when the protesters stopped a stage going into Bilbao.
“So there was always a contingency in place and the riders all voted to ride into Madrid. They knew something may happen.”
The protests come in the wake of the Israeli military launching a campaign in Gaza in response to the Hamas-led attack on southern Israel on 7 October 2023, in which about 1,200 people were killed and 251 others were taken hostage.
At least 64,871 people have been killed in Israeli attacks in Gaza since then, according to the territory’s Hamas-run health ministry.
Speaking before Sunday’s final stage, Spanish Prime Minister Pedro Sanchez said he admired the protesters.
“Today marks the end of the Vuelta,” Sanchez told a socialist party rally in the southern city of Malaga. “Our respect and recognition for the athletes and our admiration for the Spanish people who are mobilising for just causes like Palestine.”
Madrid’s mayor, Jose Luis Martinez-Almeida, said Sanchez’s comments were to blame for causing the abandonment.
“[It is] violence that the prime minister is directly responsible for due to his statements this morning instigating the protests,” he said.
“Today is the saddest day since I became mayor of this great city.”
