The Argentine, who joined the Catalan club from Man City during the summer, went down four minutes before half-time at the Camp Nou in clear discomfort and the club's medical team rushed onto the field with a stretcher.
Fortunately, the 33-year-old did not need to use it but pictures of the crowd at the stadium clearly looked disturbed by the alarming incident.
Aguero was hastily taken to hospital in an ambulance while the game reached its conclusion.
In the match, which finished 1-1, Memphis Depay opened with a superb curling strike before Luis Rioja earned Alaves a point after rounding keeper Marc-Andre ter Stegen.
It was the first match since Ronald Koeman was sacked as manager and interim coach Sergi Barjuan was unable to steer the club to victory.
Xavi is the hot favourite to succeed the Dutchman but he insisted he is "fully focused" on current club Al Sadd's upcoming matches amid speculation over the vacant position earlier this week.
At a press conference on Friday, Barca president Joan Laporta admitted he had been in contact with Xavi during the last month and talked up the coaching qualities of the four-time Champions League winner.
But Al Sadd responded ahead of their Qatar Stars League fixture with Al Ahli on Saturday.
A statement on its official Twitter account read: "In response to what's circulating recently, the Al Sadd management reaffirms that Xavi has a two-year contract with the club and is fully focused on the team's upcoming matches, to maintain our lead at the top of the league and to defend the title."
Xavi progressed through Barcelona's La Masia academy and spent 17 years as a first-teamer at the Nou Camp - eventually going on to captain the team and become one of the most decorated players in the club's history - before he left in 2015 to join Al Sadd initially as a player.