Aru just needed to get through the 98.8km parade through the streets of Madrid unscathed after building up a 1min 17sec lead over Joaquim Rodriguez on Saturday's penultimate stage.
Rodriguez finished second to record his third podium finish in the Vuelta, but a puncture midway through the stage saw him lose out on the green points jersey to Spanish compatriot Alejandro Valverde.
Poland's Rafal Majka finished third.
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