The South Americans were reduced to 10 men in the third minute when Carlos Sanchez was sent off for using his arm inside the penalty area to block a Shinji Kagawa shot, reported Xinhua news agency.
Kagawa converted the resultant penalty before Juan Quintero equalized with a free kick under the wall just before halftime.
But Yuya Osako restored the lead for Japan with a 73rd minute header and the Blue Samurai withstood a late Colombia charge to secure revenge for their 4-1 defeat in Brazil four years ago.
"It's painful for us because we came into the match with a lot of hope," Pekerman told a news conference.
"The positive side of all this is that you could see the team managed to rise to the occasion and managed to get a draw... that's a very good reaction," the Argentine added. "If we can do that it shows that we have the wherewithal to move forward with the other matches and even win them. We can make up for this first defeat in the next two matches."
Colombia started the match without Bayern Munich midfielder James Rodriguez, who is struggling to overcome a calf problem.
The 26-year-old, the leading scorer at the 2014 World Cup with six goals, was introduced in the second half and looked untroubled by the injury. Pekerman did not say whether Rodriguez would start in Colombia's next match against Poland on Sunday.
Colombia will likely need to win that match and their last Group H fixture against Senegal to progress to the knockout stage.
"Right now our pain is precisely because after that huge effort after scoring that goal... we lost because we were worn down, we were tired and even if I tried subbing on a couple of fresh players it was very hard for us to recover possession and Japan had its opportunities," Pekerman said.
"This is going to leave us with a bitter memory."
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
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