"Did you not see what just happened?" he asked journalists afterwards. "It was a handball and I'm not happy."
It was a dramatic night at the Estadio Metropolitano in Barranquilla with heavy rain causing the kick-off to be delayed and further disruptions brought by a floodlight failure at half-time and treatment for Colombia goalkeeper David Ospina's second-half head injury.
The eventual outcome means Colombia are only behind qualifying-group leaders Argentina on goal difference and can secure a place at Brazil 2014 with two points from their remaining three games. Despite the defeat, Valencia and Ecuador remain on course to get at least a play-off spot after sixth-placed Venezuela lost 3-0 away to Chile.
Angelo Henriquez played a small part in Chile's triumph in Santiago, notably making his World Cup qualifying debut. The young United striker, currently on loan at Real Zaragoza, came on for the final few minutes and was therefore on the pitch when Arturo Vidal wrapped up the victory following strikes by Eduardo Vargas and Marcos Gonzalez inside the first half-hour.
Chile's next fixture is a friendly with Spain in Geneva but they are closing in on a finals spot in Brazil with the worst case scenario currently a play-off against Jordan or Uzbekistan.