The South Americans also secured a place in the last eight of the tournament as runners up in Group B, where they will face host nation Brazil.
A first-half strike from captain Teofilo Gutierrez and a second-half penalty from Dorlan Pabon ensured that the Los Cafeteros joined their West African opponents in the quarter-finals.
Despite securing top spot before the game, Dream Team VI head coach, Samson Siasia surprisingly named Captain Mikel Obi and topscorer Oghenekaro Etebo in the starting lineup, with the later picking up an injury.
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Colombia needed a win to book their place in the knockout stage, and they were rewarded with an early lead through their captain Gutierrez, who volleyed home a fine finish past the Nigeria goalkeeper Daniel Akpeyi to Colombia the advantage.
Nigeria threatened through Etebo but the former Warri Wolves player’s effort was comfortably saved by Cristian Bonilla in goal for Colombia.
Colombia doubled their lead in the second half after Daniel Akpeyi brought down Preciado, with Pabon converting the resultant penalty to give his side a two-goal cushion.
The South Americans could have had a third goal in the 73rd minute but Preciado was unable to find the target from close range
The win earned Colombia a quarterfinal spot against Brazil in Sao Paulo, Samson Siasia and his team will travel to Salvador to face Denmark on Saturday.