The talismanic forward continued his blistering form, taking his tally to 10 goals in all competitions this season with a diving header in the eighth minute of the Primera Division encounter at the Nou Camp.
Messi also added an assist for Barca's fourth goal before being hauled off nine minutes from the end in place of Sergi Roberto.
The Argentina winger admitted he was unhappy at his substitution, but refutes media suggestions that he deliberately snubbed Martino whilst being withdrawn.
"At no point did I make any gesture when Martino took me off," Messi said on his official Facebook page.
"Nobody likes to be out, but we must accept it because it is the best for our team. What I will not accept is that certain media tell lies about any situation that happens around me."
Fellow Argentinian Javier Mascherano, meanwhile, was also substituted in the comfortable win over Sociedad after suffering a hamstring injury in the first half.
The 29-year-old was replaced by Marc Bartra in the 35th minute and Barcelona confirmed on their official website that the defender will undergo additional tests on Wednesday to determine the extent of his injury.