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The much-criticised Andre Gomes and Paco Alcacer also bagged doubles, while Javier Mascherano scored his first Barca goal in seven years with the club from the penalty spot.
Madrid have two games in hand and can move back level on points with victory at Deportivo la Coruna later on Wednesday.
Osasuna remain rock-bottom and will be relegated if Leganes beat Las Palmas on Wednesday.
Messi's brilliance against Madrid at the weekend El Clasico kept Barca in the title race as he netted his 500th Barca goal with the last kick of the game to hand the Catalans a 3-2 win.