However, two late errors by Colombian keeper David Ospina, combined with a number of missed chances by the home side, allowed Paraguay to keep their own hopes alive.
Ospina spilled the ball from a hopeful punt with two minutes remaining, allowing Oscar Cardozo to latch on to the loose ball and fire home.
A minute into injury time the keeper failed to hold a low drive and Antonio Sanabria slotted home to give the visitors three points.
The result means Colombia drop to fourth in the 10-team group, while Paraguay are in seventh. The top four teams qualify automatically for Russia and the fifth-placed side take on New Zealand in a play-off.
Leaders Brazil (38) have already qualified and second-placed Uruguay (28) need just a point to join them.
Two points then separate third-placed Chile (26) to Paraguay in seventh ahead of the final round of matches on Oct. 10.
Paraguay take on Venezuela at home, Brazil play Chile in Sao Paulo while two-time world champions Uruguay host Bolivia.
Sixth-placed Argentina, who drew 0-0 with Peru in Buenos Aires, go to Ecuador, while Peru, who occupy the playoff spot, will aim to reach the finals for the first time since 1982 when they take on Colombia.
(Reporting by Andrew Downie; Editing by Greg Stutchbury)
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