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.
Edinson Cavani scored the only goal as Uruguay put their World Cup qualifying campaign back on track with a 1-0 away win over Venezuela.
The Copa America holders, who had taken only two points from their previous six matches, climbed into the fifth-place play-off berth trading places with Venezuela on goal difference.
The top four teams in the nine-nation group will go through to the finals in Brazil next year and the fifth-placed side into a playoff against an Asian qualifier for another berth.
Uruguay, without suspended top scorer Luis Suarez, took the lead in the 28th minute from a quick break when Cavani cut inside defender Gabriel Cichero, leaving him sprawling on the ground, and hit a shot inside the far post.
Cavani was wasteful with a chance a minute later shooting wide while Diego Forlan shot over the bar in the 39th minute.
Venezuela had tested the Uruguay defence in the 18th minute with a free kick by midfielder Juan Arango that goalkeeper Fernando Muslera failed to hold and the defence scrambled away for a corner.
The home side pressed for an equaliser throughout the second half but failed to really trouble Muslera and the massed ranks of Uruguay's defence in a match played in wet conditions at the Cachamay in Puerto Ordaz.
Venezuela had midfielder Tomas Rincon sent off six minutes from time for a second booking.
Colombia, helped by another Radamel Falcao goal, produced a typically dominant performance to beat Peru 2-0, and move closer to their first World Cup since 1998.
Falcao converted an early penalty, his seventh goal of the campaign, to give Colombia their fourth successive home win in the South American qualifying group, all of them without conceding a goal.
Teofilo Gutierrez bundled in the second on the stroke of halftime as Peru continued a dismal away record which could ultimately wreck their chances of a first World Cup appearance since 1982.
Colombia, who have won seven of their 12 matches, are second in the nine-team group with 23 points and look almost certain to qualify.
Peru are sixth with 14 points and still have an outside chance, despite taking only one point from their six away matches.
With heavy rain and overcast skies making the Caribbean port even steamier than usual, Colombia took the lead with the first real chance.
Juan Camilo Zuniga was brought down by Victor Yotun and Falcao fired home from the spot.
Jefferson Farfan, surprisingly left out of Peru's starting line-up, was one of two players brought on after half an hour for the visitors as coach Sergio Markarian tried to bring his team to life.
Farfan quickly responded by firing a free kick against the post, Peru's best effort of the game.
With Peru threatening to come back into the match, Colombia struck a crucial blow when Gutierrez turned in Pablo Armero's cross on the stroke of halftime Peru made a lively start to the second half but it did not last and they had defender Carlos Zambrano sent off after a second booking in the 70th minute while seven other players were given yellow cards in an often niggly match.
Chile marked David Pizarro's comeback after almost eight years and Alexis Sanchez's first goal in the World Cup qualifiers with a 3-1 home win over Bolivia.
The victory consolidated Chile's hold on fourth place in the South American group with 21 points from 13 matches, behind Ecuador on goal difference.
Striker Eduardo Vargas scored in Chile's first dangerous approach from a cross by Eugenio Mena in the 16th minute.
The Chile fans were still celebrating when Sanchez doubled the advantage two minutes later with a header from the rebound of a shot by midfielder Arturo Vidal that hit the bar.
It was Sanchez's first international goals in almost two years. His last goal was in July 2011 at the Copa America in Argentina.
Pizarro, who had turned his back on the national team over other players' indiscipline and then refused several previous recalls, was important as playmaker, generating space and delivering deep crosses to the forwards.
Bolivia pulled one back when striker Marcelo Martins scored after the half hour mark, but the visitors never troubled Chile goalkeeper Claudio Bravo again in the first half.
Chile stepped back a few metres in the second half and allowed Bolivia to create some chances but they regained prominence and justified the victory.
Pizarro almost scored near the end with a long distance effort before Vidal headed a Jean Beausejour cross home in added time to seal the result.
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.