Colombia have dropped to seventh on the South American table, having lost 3-0 at home to Uruguay and 6-1 to Ecuador during the recent international break.
Only the top four teams on the table are guaranteed automatic qualification to FIFA’s flagship tournament.
Queiroz was appointed Colombia manager in February 2019.
"The Colombian Football Federation and the technical director Carlos Queiroz agreed the coach would not continue as head of the Colombian Men's National Team," a statement read.
"For the FCF, it was a pride to have [Queiroz] for almost two years, in which he gave us his full capacity, knowledge and experience.
"The contribution that you leave us will serve to continue the development of the projects that are being carried out with all the national teams of our country.
"We wish Professor Carlos Queiroz and his team the best in their future career plans.
"As of this date, the Executive Committee of the Colombian Soccer Federation will initiate the process to search for the coach who will occupy, in the immediate future, the position of technical director of the Colombian Senior Men's National Team."
Queiroz was formerly an assistant manager to Sir Alex Ferguson at Manchester United and the 67-year-old has also taken charge of Real Madrid and the national teams of Portugal and Iran in the past.
