Messi has not trained since returning from international duty with Argentina but is in the squad for the clash at the Calderon, which pits the champions against the 2013-14 title winners.
Spanish media reported that Messi was absent due to the birth of his second son, although there was no immediate confirmation from the club or the four-times world player of the year.
"Leo had the coach's and the club's permission to miss training for personal reasons," Luis Enrique told a news conference.
"He is in the squad and tomorrow he will be available to play," added the former Barca and Spain midfielder.
"We know the performance we and the players are capable of and we'll see what happens tomorrow at the Calderon."
Barca and Atletico both won their opening two matches of the season without conceding a goal and are level at the top on six points with Celta Vigo and Eibar.
Barca are likely to be without suspended centre back Gerard Pique on Saturday, unless an appeal against the sanction is successful.
Chile goalkeeper Claudio Bravo has been sidelined by a calf injury and will probably be replaced by German international Marc-Andre ter Stegen.
(Writing by Iain Rogers, editing by Ed Osmond)
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