Aguero has returned from a calf problem to feature in his side's last two matches off the bench, but the Argentina international has not been deemed fit enough to start the La Liga contest.
Fati, though, has been named in the starting side, with the 18-year-old set to play in his sixth match of the season, having overcome a long-term knee problem.
Sergino Dest has impressed in a more advanced role for Ronald Koeman's side in recent games, and the United States international has again been selected in a front three alongside Memphis Depay and Fati.
Dest's spot further forward means that there is another start at right-back for Oscar Mingueza, while Eric Garcia is chosen alongside Gerard Pique in the middle, with Jordi Alba, who had emerged as a doubt for the contest due to a foot injury, passed fit to feature at left-back.
Barcelona XI: Ter Stegen; Mingueza, Pique, Garcia, Alba; F de Jong, Busquets, Gavi; Dest, Memphis, Fati