Toure gave the home side a third minute lead from the penalty spot before Rickie Lambert equalized with a spot-kick of his own. However, goals from Samir Nasir and Edin Dzeko in stoppage-time of the first half proved decisive, with City substitute Stevan Jovetic completed the scoring nine minutes from time.
The victory, which keeps pressure on Premier League title rivals Chelsea and Liverpool, moves Manuel Pellegrini’s men to within one point of Liverpool at the top of the Premier League table, with the Citizens still having a game in hand.
A fourth defeat in Southampton’s last five away trips, meanwhile, hinders their late run for the top six.
The bad news is the serious-looking knee injury suffered by Southampton and England striker Jay Rodriguez and his World Cup dream could be over after falling and twisting his knee on 23rd minute in a game watched by the Three Lions Boss Roy Hodgson.
Match facts
Man City (4-2-3-1): Hart , Zabaleta, Kompany, Demichelis, Kolarov, Navas, Fernandinho (Garcia, 45), Toure, Nasri, Silva (Jovetic, 77), Dzeko (Negredo, 65).
Subs not used: Richards, Lescott, Milner, Pantilimon.
Booked: Fernandinho, Javi Garcia, Toure.
Goals: Toure (pen) 3, Nasri 45, Dzeko 45, Jovetic 81
Southampton (4-5-1): Gazzaniga, Chambers, Fonte, Lovren, Shaw, Cork (Wanyama, 80), Schneiderlin, S. Davis (Gallagher, 75), Lallana, Rodriguez (Ward-Prowse 26), Lambert.
Subs not used: Clyne, Do Prado, Hooiveld, Cropper.
Goals: Lambert (pen) 37.
Referee: Chris Foy
Attendance: 47,009
Sokka.
