Both sides had a number of opportunities during an end-to-end contest, but Messi's second-half spot kick following a Javi Lopez handball proved the difference in an ill-tempered derby.
It got worse for the home side late on when goalkeeper Kiko Casilla was sent from the field for handling outside the box, with midfielder Lopez given the gloves for the final few minutes.
Here, Sports Mole dissects the 90 minutes of action between the two Spanish rivals.
On target: 1
On target: 8
Was the result fair?
Espanyol will certainly feel that they deserved something from their efforts this afternoon, but they managed just one shot on target during the contest. Like Barcelona, the home side had chances during an end-to-end first period, but hardly threatened Jose Pinto in the second 45 minutes. A point would have perhaps been a fair result when taking into account the match as a whole, but only one team ever looked likely to win the match - and that was Barcelona.
It was a typical performance from Espanyol this afternoon. They were full of energy and pressing in midfield areas, while Sergio Garcia proved a valuable outlet in the final third. Their defence can also be credited for an impressive second half, but a late mistake from Javi Lopez cost Javier Aguirre's side the chance to take something from the match. For all their positive work in the middle of the pitch, they just did not do enough in the final third, with Barcelona goalkeeper Pinto largely a spectator. In truth, their challenge ended after 84 minutes when Casilla was sent from the field, with Barcelona threatening to add to their tally in the latter stages.
Barcelona have been in fine form in recent weeks, with victory in El Clasico last weekend capping an impressive period of the season. However, it just did not happen in forward areas this afternoon. They did have three or four golden chances in the first period, but struggled for invention in the second half. It was far from vintage, but it is results and not performances that are vital at this stage of the season. Aside from a couple of moments in the first period, Barcelona's defence were untroubled, however, and it was up to one of their forward players to make the difference. The decisive goal eventually arrived from the penalty spot, but it was a match that the away side dominated for long spells.
Sports Mole's man of the match
Jordi Alba: In truth, it was not really a match full of star performers. However, Alba stood out for Barcelona this afternoon, with the left-back always available in the final third. The Spanish international's pace caused problems to the home side in advanced areas, while he was always comfortable in defensive areas. It did not quite happen for Dani Alves on the opposite side, which made Alba's performance even more important for Barcelona.
Barcelona forward Neymar had a wonderful chance to send his side into the lead in the early stages of the first period following a driven low cross from Alves, but somehow the Brazilian fired high and wide from barely three yards out. Javi Lopez and Casilla did not cover themselves in glory in the latter stages for Espanyol, but Neymar's miss was arguably the worst of the entire season.
It was a busy 90 minutes for referee Clos Gomez this afternoon, with the Spaniard issuing six yellow cards, one red and awarding a late penalty. However, both of the big calls were correct. Barcelona's penalty arrived following a clear handball from Javi Lopez, while Casilla simply had to be sent from the field after handling a Messi effort outside the box. It was an ill-tempered affair between the two rivals, but Gomez was on hand to calm proceedings. The official was also sensitive to the nature of the occasion and only looked to his pocket when absolutely necessary.
Espanyol: Aguirre's side return to La Liga action away to in-form Sevilla next Sunday.
Barcelona: The Catalan outfit are in Champions League quarter-final action on Tuesday as they welcome La Liga title rivals Atletico Madrid to the Camp Nou for the first leg.