The brilliant Argentine forward made an instant impact when he came on for the last 30 minutes of the midweek King's Cup tie against Getafe after being out for almost two months with a hamstring injury.
Messi grabbed two goals in the 4-0 win but coach Gerardo Martino is not sure if second-placed Atletico will represent too tough a 90-minute test.
"He looks fine and had a phenomenal 30 minutes in the Cup but he returned after a long time out and the question is whether he is now ready to play a full game at this level," Martino told reporters on Friday.
"We will make a decision tomorrow. It's not really a case of asking a player how he feels as they will usually say 'fine'.
"I have to go by my sensations and look at different aspects to make a decision which people will judge me on. I am the Barcelona coach and pick my XI and then afterwards a decision will be made on how well I do," added Martino.
The coach said he might have been prepared to risk Messi if the Atletico game was later in the season.
"With injuries I usually think about the player first and then about the opposition," he said.
"We are not at a decisive moment like in April...we are in January and the priority at the moment is the players and not the result."
Coach Diego Simeone's Atletico have a 100 percent league record at home this season.
"Atletico are a strong side and I would say that from June to December they were the most solid side in Europe, not just Spain," said Martino.
"Barca as an institution are always expected to win but this will be an even battle and it should be entertaining to watch.
"We cannot ignore how the game went last time but we don't know whether it will be a similar match or other elements will influence it," added Martino, referring to the 1-1 draw at Atletico in the Spanish Super Cup first leg in August.
"We need to be more precise and open up our play more. It is a different situation to last summer.
"We are better than we were five months ago physically and psychologically, we have been improving while Atletico have never dropped their level," said Martino.
Both teams have 49 points from 18 games but Martino does not believe Saturday's game will be decisive in the title race.
"I don't think it will be with half the matches still to go," he said.