The former Manchester City striker Aguero went down holding onto the top of his chest and received treatment for several minutes before being helped off the pitch just before half-time.
Barcelona later said he was admitted to hospital to have a "cardiac exam".
Luis Rioja earned Alaves a point after Memphis Depay's opening curling effort.
Former Manchester City striker Aguero, 33, was taken away in an ambulance and Barca interim boss Sergi Barjuan told La Liga TV: "I can't tell you much more. I know he has been taken to a hospital and they are having tests done."
The Argentine was making his first start for the club since his move in the summer.
Source: Tribalfootball
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