Liverpool, who have travelled well this season, had much of the play in the opening period but were unable to create many chances and failed to convert any they did.
The visitors had less control of the game after the break as Roberto Mancini's men looked to secure the points.
Gareth Barry was dismissed for a second bookable offence before Toure surged forward in typical fashion and was brought down by Martin Skrtel. Milner stepped up and sidefooted the ball into the top corner confidently.
City, who have now won all ten of their home Premier League games this season, move three points clear of Manchester United. The Red Devils play their game in-hand at Newcastle tomorrow.