Messi missed a golden chance in the first half but set up Rodrigo De Paul five minutes before halftime and then did the same for Lautaro Martinez five minutes from the end.
The Barcelona player then got his second freekick of the tournament in stoppage time to round off a scoreline that was more convincing than the performance.
The result means Argentina will face Colombia, who overcame Uruguay on penalties earlier in the day, in the second Copa America semifinal on Tuesday.
Brazil play Peru in the first semifinal 24 hours before.
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