Porto star Radamel Falcao scored in the 15th and 29th minutes for Colombia to secure top spot in Group A with 7 points. Bolivia finished with only 1 point and was eliminated.
Colombia will face the best third-place team in the quarterfinals. The top two teams in each group reach the quarterfinals, joined by the best two third-place teams.
Peru, Chile and Venezuela, which have 4 points after two matches, also advance to the knockout stage.
Tournament favorites Argentina and Brazil have only two points in two matches and will advance if they win their final group matches.
Argentina faces Costa Rica on Monday and Brazil plays Ecuador on Wednesday.