The 29-year old midfielder suffered a broken bone in his foot in a 3-0 win over Chelsea in the Champions League and will be out of action for close to three weeks.
Despite only winning eight league matches this season, they are comfortably away from the relegation zone at present and will have an eye on potentially challenging for the European places during the business months of the campaign, not least now they're out of the Europa League and can exclusively focus on their league performances.
Just four days after an encounter with Chelsea that was more exacting than the 3-0 scoreline suggested, the intensity understandably dropped in the second half, but Valverde's men were able to keep Athletic at arm's length to ensure they head into the global break in buoyant mood.
Messi then forced Bilbao goalkeeper Kepa into a fine save moments later, before Philippe Coutinho saw a shot cannon against the crossbar in the 15th minute.
A swift move was finished off when Jordi Alba cut back from the left for Alcacer to slot home calmly into the bottom-right corner.
Indeed, when the visitors did finally get a shot on goal in the 69th minute, Raul Garcia knew very little about the attempt as Enric Saborit's effort clipped his heels and was easily taken by Marc-Andre ter Stegen.
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Barcelona forward Paco Alcacer has described himself as a "team player" after making the most of his rare start against Athletic Bilbao.
In their last ten, Bilbao have only recorded two victories and drawn five - their lack of consistency is why they're not higher in the table at present.
Lionel Messi is the inspiration behind Barcelona's charge towards a possible treble of LaLiga, Champions League and Copa del Rey titles, according to Paco Alcacer.
Athletic dropped to 13th in the 20-team standings.
- Excluding direct free-kick goals, Messi has scored his first goal from outside the box in La Liga this season.
Athletic, meanwhile, have not won at the Camp Nou in any competition since November 2001 - a run of 21 games. Only against Sevilla (19) and Espanyol (18) has the Argentine player netted more goals for Barcelona.