More than 82,000 fans attended the friendly in Arlington, Texas and it looked like the majority of the crowd would go home happy after Javier Hernandez put away a 19th-minute penalty and Hector Herrera doubled El Tri’s advantage on 70 minutes.
But Aguero, who replaced former City team-mate Carlos Tevez after 76 minutes, turned in a Ezequiel Lavezzi cross on 85 minutes before picking out the run of Messi with a sumptuous 25-yard chip and the Barcelona man did the rest with just one minute of normal time remaining.
Nicolas Otamendi and Martin Demichelis both got a useful 90 minutes under their belt ahead of a busy week back in Manchester.
Elsewhere, Fabian Delph looks set for a spell on the sidelines after limping out of England’s 2-0 win over Switzerland.spell on the sidelines after limping out of England’s 2-0 win over Switzerland.
The former Aston Villa midfielder lasted less than a minute when he appeared to pull up with what could be a hamstring injury - though there has been no official confirmation as yet.
Delph, who was injured early in his City debut against Real Madrid in pre-season, lasted less than a minute before sitting down on the Wembley turf unable to run.
He walked off rather than being stretchered and was replaced by Ross Barkley of Everton, but it seems unlikely he will be available for City’s upcoming games with Crystal Palace and Juventus.
In a somewhat muted game, England went into the break 0-0 thanks to a fine save from Joe Hart on 31 minutes before gradually taking control of the game in the second-half when Harry Kane finally broke the deadlock on 67 minutes.
Raheem Sterling had enjoyed a steady evening but it was his trickery in the box that won an 84th-minute penalty that was converted by Wayne Rooney - his 50th for England breaking Sir Bobby Charlton’s long-standing record.
That completed a 2-0 win and preserved the Three Lions’ 100% qualifying record so far.
In Macedonia, David Silva gave his usual assured performance as Spain edged a 1-0 victory to move two points clear of Slovakia at the top of Group C.
Juan Mata scored the only goal of the game on eight minutes as La Roja all-but booked their place at next summer’s finals.
