The Argentine forward spent Friday night and Saturday morning being sick and the decision was taken for him to miss the game at Camp Nou just hours before kick-off.
However, the worst of the illness had passed by Sunday and Messi has now returned to training with his teammates ahead of Wednesday's Champions League game against Celtic.
Luis Suarez, who missed the Malaga game due to a suspension, also trained and should reclaim his place in the starting lineup in Glasgow alongside Messi and Neymar.
Luis Enrique is also expected to bring Jordi Alba back into the starting lineup. The left-back came off the bench at the weekend after recovering from a hamstring problem and should force Lucas Digne onto the bench at Celtic Park.
⚽️ Entrenamiento de los jugadores disponibles del primer equipo en la Ciudad Deportiva. También entrenan Marlon, Paik y Mujica del Barça B pic.twitter.com/VXcWcVC4QO
- FC Barcelona (@FCBarcelona_es) November 21, 2016
Like Alba, Gerard Pique also returned against Malaga, coming through 90 minutes and showing no ill effects of the ankle injury which sidelined him for three weeks.
Jeremy Mathieu may also come into contention, but Barca will once again be without captain Andres Iniesta and defender Samuel Umtiti.
Iniesta's recovery is ahead of schedule, Luis Enrique revealed last week, and both he and Umtiti could return in time for the Clasico against Real Madrid on Dec. 3.
Following the 0-0 draw with Malaga, the Blaugrana have fallen four points behind Madrid at the top of La Liga, while heading into their game with Celtic they lead their Champions League group from Manchester City by two points.