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.
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.
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.”