The South Americans took the game to extra time at the Spartak Stadium after salvaging a goal in the final stages of the contest through Yerry Mina, before the Three Lions won it on penalties.
American referee Mark Geiger lost control of the scrappy match early on, with Colombia's players repeatedly getting in his face to dispute decisions - most notably Kane's penalty.
Pekerman claims that his side were hard done by as England's players attempted to con the official, and he expects more to be done when Gareth Southgate's men face Sweden in the quarter-finals.
"Players fall in the box, they collide and fall," he told reporters after the match. "You have to try and stand in the shoes of these players. They are subject to situations which shouldn't really be present in football.
"These interruptions are bad. When there are so, so many fouls and interruptions I think that's not good. We have to try and find the right balance so that football can happen and the two sides can play the match with good intentions.
"We shouldn't only look at Colombian players, people should look at England players. I wish I was wrong, but I think from the next match England will be much more careful.
"Today we were on the receiving end of this but I hope it won't happen again. It's been absolutely obvious, too obvious."
Colombia have lost three of their four knockout matches at the World Cup, having previously been dumped out at this stage in 1990 and in the last eight four years ago.