The world's most expensive player added to Asier Illaramendi's first-half opener with a stunning strike on 71 minutes, and then substitute Isco hit a third with 10 minutes remaining.
Title rivals Barcelona endured another miserable trip to the Anoeta on Saturday night as Real Sociedad produced a brilliant team display to beat the under-par Catalan giants 3-1.
The Basque outfit, who defeated Barcelona 3-2 in the corresponding fixture last term, went ahead in the 32nd minute when Gorka Elustondo's header found the net via the shoulder of visiting defender Alex Song.
Lionel Messi equalised four minutes later with a typically clinical finish, but further home goals in the first 14 minutes of the second half - scored by Antoine Griezmann and David Zurutuza - ensured the Primera Division champions left San Sebastian empty-handed for the third time in four seasons.