Colombia was unbeaten after six games, but back-to-back losses to Uruguay (1-0) and Chile (4-0) made Pinto the third coaching victim of the South American qualifiers on Tuesday.
Youth coach Eduardo Lara will take over for Colombia, which dropped to sixth place with 10 points after eight games and must play at home against leader Paraguay and away to Brazil next month.
The top four teams qualify for the World Cup and the fifth plays off against Concacaf's No. 4 team for another place.
Ecuador and Venezuela have also changed coaches since the competition began.