City had three efforts cleared from the line and there were bad misses from Sun Jihai, Shaun Wright-Phillips and Nicolas Anelka.
Southampton were happy simply to survive to half time and although they improved after the break a point was as much as they deserved.
Head coach Steve Wigley is still looking for his first league win in charge and his record now stands at two points out of a possible 18.
Manchester City forced 13 corners and had enough shots on target to have gone home happy but in the end they were holding on with increasing difficulty and in the dying seconds almost paid for their mistakes when Kevin Phillips saw his lobbed shot held at full stretch by David James.
Defenders Richard Dunne and Sylvain Distin each had efforts cleared from the line by David Prutton following corners on the right by Anelka and Southampton suffered another blow when James Beattie limped off with a suspected broken toe after only 18 minutes.
Ben Thatcher saw a left foot free kick from 25 yards drift just over the bar and then Anders Svensson was again positioned on the line to clear away another towering header from Dunne, from another Anelka corner.
Sun Jihai had the games best chance after 35 minutes but his left foot shot drifted across the face of the goal when a score looked certain and it was not until four minutes before the break that Southampton at last showed attacking intent but a header from Phillips was saved on his line by James.
Jelle Van Damme came on in place of the injured Graeme Le Saux at the start of the second half and this time it was City's turn to be relieved to find a defender on the line, Dunne clearing away a header from Rory Delap.
But the better chances continued to fall to Manchester City and Sun Jihai saw a fierce shot brilliantly saved by the over worked Antti Niemi.
Niemi gave Southampton another scare in the 69th minute when Niemi was injured in bravely rushing from his line to block a shot from Anelka, but he was fit again six minutes later when he kept out a low shot from Jonathan Macken from 12 yards.
Peter Crouch, an 18th minute substitute for Beattie, had a header saved by James and then came the Phillips miss as both sides pressed for a winner.
Wigley sent on Neil McCann in place of Fabrice Fernandes after 67 minutes in a bid to snatch a winner but it made little difference as Manchester City went forward with the greater purpose.
England's Shaun Wright-Phillips, who otherwise had a quiet afternoon, also let off Southampton with a shot across the face of the goal with Niemi beaten but Southampton were able to pick up a useful point.