Luis Suarez and Philippe Coutinho scored as Barcelona beat Malaga 2-0 on Saturday evening at La Rosaleda.
Messi, who has netted 24 goals in 27 league games, was left out of the squad after the birth of his third son on Friday evening.
Malaga were the last team to beat Barca, securing a 1-0 win last season as Ernesto Valverde’s side lost the league title to Real Madrid.
But, Barca were brilliant as they moved past bottom placed Malaga thanks to goals from Suarez and the excellent, Coutinho.
Suarez’s header after a delightful ball from Jordi Alba gave the Catalan side the lead, before Coutinho’s excellent backheel ensured all three points would be heading back to Catalonia.
Malaga played an hour with ten-men after Samu Garcia was sent off for a disgusting foul on Alba, but Barca chose not to push on and add more goals – using the second half to relax and prepare for the Wednesday fixture against Chelsea in the Champions League.
Wednesday’s game is delicately poised after the 1-1 first leg at Stamford Bridge, which saw Messi cancel out Willian’s goal.
Malaga are 11 points from safety in La Liga with just 10 games remaining, whilst Barca sit eight points clear of title rivals Atletico Madrid.