Oliveira jumped away from a group of 24 riders in a descent with 27 kilometres remaining and never looked back.
The 26-year-old, his country's time trial champion, crossed the line one minute ahead of the chasers, according to provisional results.
France's Julien Simon (Cofidis) was second and Ireland's Nicolas Roche (Sky) took third place at the end of a 178-km ride from Calatayud to Tarazona.
Overall leader Fabio Aru of Italy finished safe in the main pack, almost five minutes off the pace, to retain the red jersey.
He still leads Spain's Joaquim Rodriguez (Katusha) and Dutchman Tom Dumoulin (Giant-Alpecin) by 27 and 30 seconds respectively.
A big battle between the top guns looms on Saturday as the 14th stage is a tough moutainous ride between Vitoria and Fuente del Chivo.
(Reporting by Julien Pretot; Editing by Justin Palmer)
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