The Colombians celebrated as though they had secured their ticket to next year's tournament in Brazil, but have ensured only that, at worst, they will go into a play-off against an Asian qualifier in November.
They joined Argentina at the top of the South American group from which the leading four teams will go through to the finals at the end of the qualifying campaign next month with the fifth-placed team reaching the play-off for one more berth.
Midfielder James Rodriguez scored the only goal after half an hour when Ecuador were already down to 10 men after defender Gabriel Achilier was sent off for bringing down goal-bound striker Teofilo Gutierrez in the 28th minute.
Striker Radamel Falcao, passed fit at the last minute, had a shot from outside the box which goalkeeper Maximo Banguera could only parry away, allowing his Monaco team mate Rodriguez to swoop in from the left and steer a left-footed shot in off the base of the far post.
"I'm happy with the goal and because we won. When you want to win things you also have to suffer and that happened today," Rodriguez said after Colombia laboured against a team a man short for more than an hour.
Ecuador should have equalised just past the hour but left back Walter Ayovi put his penalty wide after Antonio Valencia had been brought down by Carlos Sanchez.
Seconds later at the other end midfielder Juan Cuadrado crossed from the right to Gutierrez at the far post but the ball hit the striker on the thigh and came back off the post.
The match ended three hours and 40 minutes after it had been scheduled to start.
First, kick-off was delayed due to a waterlogged Metropolitano pitch after earlier torrential rain, which abated but did not stop and the match started an hour and a half late.
Then the start of the second half was delayed for 20 minutes due a floodlighting failure.
There was also a five-minute delay early in the second half for treatment to Colombia goalkeeper David Ospina after he banged his head in a collision with Montero, though he recovered to play on.
There was a minute's silence before kick-off in remembrance of Ecuador's Christian Benitez, who died of heart failure in Qatar in July.