The protests against the presence of the Israel Premier Tech team have dogged the Vuelta, forcing stages to be shortened and stripping them of competitive or sporting value.
Riders on Sunday will cover 103.6km between Alalpardo and Madrid instead of the 111.6km planned.
The section removed would have crossed the plush Madrid neighbourhood of Aravaca 9km from the centre, organisers told media, without specifying a reason.
Madrid have ramped up security measures for the final stage of the race, with the first deputy mayor saying policing numbers would be "almost doubled".
The central government's representation in Madrid said there will be "extraordinary" reinforcements to keep riders safe, with more than 1,500 extra police officers, both municipal and national, to be deployed.
Protesters have even run out onto the course and caused crashes, among other flashpoints across the three-week race.
READ ALSO: Why Spain's top cycling race has been rocked by pro-Palestinian protests
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