The striker started for his nation against Argentina in the curtain-raiser to Sunday's final between Brazil and Peru after Chile were comprehensively beaten 3-0 by the Inca to surrender their continental title in the last four.
But he lasted barely 15 minutes of the encounter before pulling up with an apparent muscular injury, having appeared in all of the Roja's matches to date in Brazil.
Alexis was forced to hobble off the Arena Corinthians pitch, and was replaced by Junior Fernandes with his nation already a goal down after Sergio Aguero converted early.
Chile's misery was compounded within a matter of minutes when Paulo Dybala pulled off a sublime finish to make it 2-0 to Argentina, seemingly hungry for revenge after losing the last two Copa finals to their neighbours in 2015 and 2016.
While the news is a blow to his national team, those in charge at Old Trafford will also be anxiously waiting to find out the severity of the injury as they continue to plan for the coming season.
Having endured a torrid 18 months at United since moving from Arsenal at the start of 2018, Alexis is among those who could be seeking a new club this summer.
A string of impressive Copa displays would have been welcomed therefore by the Reds as they look to offload the star, whose elevated salary poses an issue when it comes to a sale.
Alexis went into the third-place play-off as one of the candidates for the Copa Golden Boot award, as one of a gaggle of players currently leading the competition scoring charts on two goals.
So far precious little interest has been shown in the 31-year-old forward, with some reports suggesting that only two tentative enquiries from China and South America have been fielded.
And the chance of a sale would take a further hit if a serious injury is now confirmed that would leave the Chilean laid up for most of the pre-season period or even longer.
Alexis has played 45 games for United in his season and a half at the club, scoring on just five occasions.