Los Angeles Galaxy midfielder dos Santos rifled home in the 73rd minute to settle a hard-fought encounter between the two arch-rivals of North American football in front of 62,493 fans.
Mexico have now won the Gold Cup eight times since 1991 when the championship for teams from North America, Central America and the Caribbean (CONCACAF) was rebooted.
It was a disappointing defeat for the American men, who had been hoping to complete a trophy double after the US women had powered to victory over the Netherlands in the World Cup in France earlier on Sunday.
"Over the course of 90 minutes, Mexico was the better team," US coach Gregg Berhalter said.