It was the second time in two days that the country's national anthem was subject to a mix-up at the tournament.
Organisers apologised for playing the Chile anthem instead of Uruguay before their game against Mexico on Sunday.
Chile went on to lose Monday's game 2-1 to the 2014 World Cup finalists.
Fans and players were still singing as the the pre-recorded anthem music ended, and, according to reports, the Pitbull track was next on the tracklist at the Levi's Stadium in Santa Clara, California.
American Pitbull has sold more than 60 million records globally - leading to his nickname 'Mr Worldwide'.
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Chile's players and fans had to compete with the music of rapper Pitbull, as it was played over the final bars of their national anthem before a Copa America match against Argentina.