Messi — who had equaled Javier Mascherano’s Argentinian caps record of 147 last week — marked his 148th appearance in style, setting up the opening goal before bagging a brace of his own.
The victory at Cuiaba’s Arena Pantanal stadium sees Argentina advance to a quarter-final on Saturday against Ecuador, the fourth-placed finishers from Group B.
Bolivia, who had already been eliminated after three defeats in their opening three games, were outclassed from the outset by a rampant Argentina.
The Argentines almost took the lead after three minutes, only for Bolivia goalkeeper Carlos Lampe to pull off a remarkable double save from Sergio Aguero and Angel Correa in quick succession.
But Argentina did not have to wait long for the breakthrough when Messi’s delightful chipped pass released Papu Gomez who volleyed past Lampe to make it 1-0 after six minutes.
Argentina doubled their lead on 33 minutes when Gomez was brought down in the area by Bolivia’s Diego Bejarano.
Messi duly stepped up to convert the penalty to put Argentina firmly in control.