A penalty from Arturo Vidal and a double from Alexis Sanchez saw Jorge Sampaoli's side race into a 3-0 lead inside the opening half-hour, but a red card for Carlos Carmona on 66 minutes changed the complexion of the match as Teo Gutierrez and two spot kicks from Radamel Falcao completed a second-half salvo in Barranquila.
The result confirms Colombia's place at Brazil 2014, marking their first appearance at a World Cup finals since 1998, and Pekerman admitted it was hard to recall an international comeback to match that of his side on Friday.
"I was surprised by what happened to us [in the first half]," Pekerman told reporters after full-time. "It could have been due the pressure accumulated over a long time.
"I'm very proud of my team, I've rarely seen a national team in this kind of match come back from 3-0 down.
"We knew beforehand this would be one of the best games of the qualifying round because of the two teams and how they've been playing. And we saw that, we saw it was exactly that.
"We also knew that both teams were capable of doing damage. Today we had two halves - one was absolutely Chile's. And the other was undoubtedly Colombia's.
"I'll repeat: I am proud of this team and what the team did. It's very difficult in football to have these two things: to have players with talent, good players, and to have this rebellious attitude and to get such a result, facing it head on. It's marvellous."Chile coach Sampaoli, meanwhile, was aggrieved at the manner in which his side surrendered their early advantage despite the result leaving them needing just a point to secure qualification.
"I'm bitter about the final result, given how things went in the first half, and now I'm hopeful as we go to seek the match that will seal our qualification," he said.
Both Chile and Ecuador currently sit on 25 points in the Conmebol table ahead of their decisive clash on Tuesday, three points above Uruguay in fifth.