In the energy-sapping thin air of Quito, the Argentines, with World Player of the Year Lionel Messi only playing for the last half hour, had their lead in the South American group cut to three points with Colombia's 2-0 home win over Peru.
Argentina have 26 points, Colombia 23 and Ecuador, who dropped their first points in seven home qualifiers at the Atahualpa where visiting teams struggle at 2,800 metres, remain third with 21.
Argentina made a quick start and Ecuador goalkeeper Alexander Dominguez could only parry Angel di Maria's stinging shot then upended Rodrigo Palacio as the striker chased the loose ball.
Aguero stepped up to send the penalty into the bottom left corner with Dominguez diving the other way.
Ecuador hit back at a free-kick near the corner flag in the 17th minute with a static defence, allowing Segundo Castillo a free header from inside the six-yard box.
"We've been making do with draws," Messi, who recently recovered from a hamstring injury, complained after Argentina's third successive stalemate result in the qualifiers. "We are closer to qualifying and that's what's important."
"We scored a quick goal and I wonder if the goalkeeper shouldn't have been sent off.
"It's difficult to play here, then they equalised," added Messi, who had also struggled in the rarefied air in La Paz, which is even higher than Quito, in the 1-1 draw with Bolivia in March.
Messi, who had also only played for half an hour in the 0-0 draw at home to Colombia on Friday, played mostly at walking pace on Tuesday, waiting to receive the ball and then attack at speed.
The home side failed to capitalise on a string of corners in both halves that the Argentine defence desperately cleared.
Argentina had midfielder Javier Mascherano shown a red card towards the end of the match in a bizarre incident off the pitch after he kicked the driver of the medical cart that took him off following a knock.
The top four teams at the end of the qualifiers in October will go through to next year's finals in Brazil.
The fifth-placed team will enter a play-off against an Asian qualifier in November for another berth.
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