The visitors began to dominate possession, but were unable to carve out a clear-cut chance.
Southampton gradually came back into the game, but Pablo Osvaldo was unable to find the target with a volley, although he was given offside.
Man City continued to search for a second goal and almost found it through Aguero. Yaya Toure clipped a ball to Pablo Zabaleta, who pulled it back for the goalscorer. However, this time Aguero's shot went over the bar.
The hosts almost found an equaliser before the break as Shaw's cross bounced along the six-yard box, but Calum Chambers was unable to get his header on target.
However, it was 1-1 three minutes before half time. Osvaldo ran down the left-hand side of the box before cutting in on his right and curling a dipping effort in off the underside of the bar.
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Manuel Pellegrini's men made the better start to the second half, with Aguero forcing Gazzaniga to save down low.
Toure then curled a shot wide after battling his way through the home defence, but Southampton went up the other end and Osvaldo ballooned his effort over.
Both teams pushed for a winner in the final minutes, but had to settle for a point apiece.