Aguero, 33, had to be taken off before half-time after being attended to on the Camp Nou pitch by Barca's medical team for a lengthy period of time.
The Argentina international was eventually able to walk off the field before being transferred to hospital where he underwent tests to determine the nature of the problem.
"The first team player Sergio Aguero reported chest discomfort and has been admitted to the hospital for a cardiac exam," Barca said in a brief statement after the game.
Aguero will continue in hospital on Sunday to undergo further exams after suffering an arrhythmia during Saturday's game.
Barca also lost Gerard Pique to a calf strain against Alaves to further increase their injury woes. Sergi Roberto, Ronald Araujo, Pedri, Frenkie de Jong, Ansu Fati, Ousmane Dembele and Martin Braithwaite all missed Saturday's game with various fitness issues.
Aguero, who joined Barca from Manchester City in the summer on a free transfer, only made his debut for the club earlier in October after he injured his calf in preseason training.
The game against Alaves marked his second start in a week as Barca's winless run stretched to three games in LaLiga.
Luis Rioja equalised almost immediately for Alaves to earn a point for the Basque side and leave Barca languishing in ninth in the league table with 16 points from 11 games.
"It's a bad point," defender Jordi Alba told reporters after the game. "Anything other than three points is bad for Barca, but especially now seeing where we are in the standings.
"We did enough but we are struggling to score and it takes very little for teams to score against us. We are all trying but it's tough."
Barjuan will remain in charge for Tuesday's must-win game against Dynamo Kiev in the Champions League as the search for a new manager goes on.
Sources have told ESPN that talks with Al Sadd coach Xavi Hernandez are at an advanced stage, but an agreement for the former midfielder to return to the club is not yet finalised.