The Argentine had missed Barca's win over Malaga at the weekend due to a thigh knock but practiced normally ahead of Wednesday's clash with Atletico Madrid.
The Argentina international was withdrawn at halftime of the first leg against Diego Simeone's side last week and was forced to sit out the weekend's 1-0 league win over Malaga. He has now been passed fit to face the capital club at Camp Nou, with the sides level at 1-1, and he practiced with his teammates Monday.
"Leo Messi was back in training with the rest of the squad this lunchtime after being rested as a precautionary measure for the game against Malaga, following the bruised thigh he suffered against Atletico Madrid last Wednesday," a club statement read.
Meanwhile, those who were involved in the narrow win at La Rosaleda did recovery work, having stayed overnight in Malaga.