Panagiotis Kone put Greece ahead on 21 minutes in New Jersey, with Kostas Katsouranis adding a second nine minutes after the interval.
Rudy Cardozo did pull one back for Bolivia 20 minutes from time, but Greece saw out the victory in their final pre-tournament friendly.
Having been drawn in a competitive-looking Group C with Colombia, Japan and Ivory Coast for the finals in Brazil, Greece will feel confident of reaching the second round for the first time in their history.
And Santos has been pleased with his side's preparations, with Friday's victory coming on the back of goalless draws with Portugal and Nigeria.
"We have seen the progress of our team," he said.
"We started in the first game with Portugal where we didn't play so well in the first half, but we could see our team was getting better and better in the remaining matches.
"The only thing that still disturbs us is that we're not pressing the opponent and stealing the ball back with as much efficiency as we want."
