Barca coach Ernesto Valverde described Messi finishing fifth as "absurd" earlier in the week and on Saturday said it was "striking" that any vote on the best in the world would not include his star man.
Barca led in the 17th minute thanks to the first moment of Messi magic in an astounding display.
Luis Suarez - back in the team following a knee problem - had the opportunity to send Barcelona two goals ahead four minutes later when he met a clever pass from Messi, but Diego Lopez was on hand to make the save.
Espanyol will be rueing the day this week that Pelé chose to weigh in on Messi's abilities.
That allowed Atletico Madrid, who recorded a comfortable 3-0 victory over fourth-placed Alaves, to briefly move level on points with the top two.
Pele said, "How can you make a comparison between a guy who heads the ball well, shoots with the left, shoots with the right and another who only shoots with one leg, only has one skill and doesn't head the ball well?"
Messi was in fine form against derby rivals Espanyol.
Lionel Messi has finally spoken out following his fifth-place finish in the Ballon d'Or standings, stating that the snub did not necessarily act as extra motivation for him. But it was Barca causing all the issues once more.
His goal means Messi has reached 10 for the season already in the league this term, becoming the first player to hit the landmark in 13 consecutive LaLiga seasons.
According to ESPN's Alexis, the five-time Ballon d'Or victor has scored more direct free-kicks than any club in Europe's top five leagues in the last four years.