Nicolas Otamendi had already powered a header past Saints' 'keeper Alex McCarthy when the Argentine striker, captain for the evening, volleyed home from six-yards after Kyle Walker’s pinpoint cross.
City, who had debutant Tommy Doyle in midfield alongside fellow Academy graduate Phil Foden, looked comfortable throughout and Aguero put the result beyond doubt as early as the 56th minute.
Riyad Mahrez carved a shooting opportunity and when his effort was deflected, City’s record goal scorer was in the right place to deftly guide the ball through McCarthy’s legs.
A Jack Stephens' header 15 minutes from time gave the visitors a glimmer of hope, but City were untroubled to see out the game.
Check out the best photos from the game in the gallery below.