Pekerman's men won their first two matches in Group C, thrashing Greece 3-0 and edging Ivory Coast 2-1, to book a knockout-stage place in Brazil.
And although it is mathematically a dead rubber for his team, Pekerman said Tuesday's battle with the Japanese at the Arena Pantanal was important.
"It is the World Cup, we have to take full advantage," the Argentine said.
"This match is very special in Cuiaba, because it is what defines many things.
"I hope to continue working hard with Colombia."
Midfielder Fredy Guarin said he was anticipating a fast-paced Japan line-up for their clash.
"I'm very excited, very happy," Guarin said.
"We all know that the most important game is now Japan, we are focused on this game.
"Japan is a very fast, attacking team."
Colombia legend Carlos Valderrama said he believed the South American nation - ranked eighth in the world, down from fifth earlier in June - could be the "surprise team" in the knockout rounds.
"Past experiences in a World Cup are always useful. It's was very important that the team know each other well," Valderrama said.
"They approached this World Cup and were very well prepared. They've played well in both games.
"For the first time ever, Colombia have qualified out of the group stage after the first two matches.
"This is also the World Cup where Colombia have scored the most goals.
"At every World Cup, there is always a surprise team, and I definitely think that this time it could be us."
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