The 59-year-old said his side were forced to pay for their mistakes and insisted they can bounce back from their opening World Cup defeat to the South Americans in Group C
Pablo Armero, Teofilo Gutierrez and James Rodriguez were on target to ensure Greece's World Cup campaign got off to a miserable start in Belo Horizonte.
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The defeat dents Greece's hopes of making it out of a World Cup group for the first time, but Santos insists all is not lost.
"It's not a tragedy," he told reporters. "It is a setback that complicates the situation.
"I will talk with my players, we will look at our mistakes to correct the situation and in the next two matches we will present ourselves better.
"Congratulations to Colombia, they were the better team and fairly won 3-0. We had opportunities, we had effort but we paid for our mistakes."
Greece will hope to turn their World Cup fortunes around when they face Japan on Wednesday before clashing with Cote d'Ivoire on June 24. The European nation's upcoming opponents face each other on Sunday.