It might have been even worse for Guardiola's side after referee Jon Moss controversially overturned decisions to award Southampton a penalty and send City defender Kyle Walker off in the second half. City had scored 16 goals in their last three home games, but the champions' usually potent attack was subdued by Southampton's well-drilled defence.
The result left City three points behind leaders Liverpool, with Manchester United and Chelsea able to go above them if they avoid defeat on Sunday.
Guardiola had irritated a section of City's fanbase by asking for more support after just 38,062 turned out at the Etihad for Wednesday's 6-3 win over Leipzig in the Champions League. That low number was partly due to the almost complete lack of Leipzig fans and the attendance was much closer to the Etihad's 55,000-capacity for Southampton's visit.