Messi missed Barcelona's training session as he was given permission to attend the birth but will be in the squad to face Atletico on Saturday.
The Argentina striker already has one son with girlfriend Antonella Roccuzzo, Thiago, who was born in 2012.
Barcelona confirmed their 18 man squad for the game against Atletico is: Ter Stegen, Masip, Rakitic, Sergio, Iniesta, Suárez, Messi, Neymar, Rafinha, Mascherano, Bartra, Munir, Jordi Alba, Sandro, Sergi Roberto, Adriano, Vermaelen and Mathieu.